SPOILERS! Mysteries and Conspiracies of Pokemon

Gee, what makes you say that?


(BTW, each word in my above sentence leads to a different link...)
Meh. The Pokedex has never bothered me, and I don't see why some people get rattled by it, even though they seem to have no problem with Pokemon shooting lightening and fire all over the place lol. Pokemon are magical beings with nuke like powers, they aren't bound by our rules of science. Trying to complain about unrealism in Pokemon would be like complaining about unrealism into other RPG's like Elder Scrolls or Dragon Age, it's a pointless endeavour, because their universes don't follow the same rules ours does.
 
Meh. The Pokedex has never bothered me, and I don't see why some people get rattled by it, even though they seem to have no problem with Pokemon shooting lightening and fire all over the place lol. Pokemon are magical beings with nuke like powers, they aren't bound by our rules of science. Trying to complain about unrealism in Pokemon would be like complaining about unrealism into other RPG's like Elder Scrolls or Dragon Age, it's a pointless endeavour, because their universes don't follow the same rules ours does.
Touché.
 

Pikachu315111

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Meh. The Pokedex has never bothered me, and I don't see why some people get rattled by it, even though they seem to have no problem with Pokemon shooting lightening and fire all over the place lol. Pokemon are magical beings with nuke like powers, they aren't bound by our rules of science. Trying to complain about unrealism in Pokemon would be like complaining about unrealism into other RPG's like Elder Scrolls or Dragon Age, it's a pointless endeavour, because their universes don't follow the same rules ours does.
But its fun :P
 
If most sci-fi universes, like my favorite Star Trek, bends the know laws of nature with their gee-whiz technology, Pokemon just takes those laws of physics, throws them out the nearest convenient airlock, and sends them on their way to the nearest quantum singularity.
 
Sorry to double post, but I wanted to add to the Jynx mystery since there is a lot to ponder about it's design (except the obvious recoloring that we won't get into).

In the anime, it had a foot once (but this is pre-retcon):
View attachment 21857
but after that it's stated only darkness is seen in it's XY and Battle Revolution models (according to Bulbapedia) and it has no Pokedex footprint.

Another mystery is these weird dress spikes that have become more prominent with each generation (really becoming noticeable in Gen 4 onward). Compare this one from Gold:

to this one in Heartgold:

to this one in XY:

Why does the dress have hip spikes? WHY GAMEFREAK, WHY?!
I never noticed the hip spikes i just thought they were part of an outer layer like you'd see on evening gowns and the like. Never really understood why GF wanted a Gangoro Girl pokemon who enjoys having her brests rubbed in pokemon-amie
 
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I don't believe we covered this already, but what happens to the pokemon that you defeat in the wild? In the games and anime(esp), when your pokemon faints or gets injured everyone starts flipping out that it needs to be healed and the whole "treat your pokemon well" theme. So let's say you are EV training on hordes with a level 100 tyranitar and are just destroying hordes upon hordes of weepinbell. What happens to those weepinbell? In the games when a pokemon faints it is, for all intensive purposes, dead until you use a revive or go to the pokemon center. So what happens to the masses of wild pokemon that you've been EV training on with tyranitar? Do they have a way of healing(reviving) on their own, and if so why don't the pokemon you own? Or do they all just die?
 
I don't believe we covered this already, but what happens to the pokemon that you defeat in the wild? In the games and anime(esp), when your pokemon faints or gets injured everyone starts flipping out that it needs to be healed and the whole "treat your pokemon well" theme. So let's say you are EV training on hordes with a level 100 tyranitar and are just destroying hordes upon hordes of weepinbell. What happens to those weepinbell? In the games when a pokemon faints it is, for all intensive purposes, dead until you use a revive or go to the pokemon center. So what happens to the masses of wild pokemon that you've been EV training on with tyranitar? Do they have a way of healing(reviving) on their own, and if so why don't the pokemon you own? Or do they all just die?
In the anime, pokemon will recover on their own over time, with access to a pokemon center only helping it go more quickly and deal with very bad injuries. Also, in the anime, wild pokemon can use pokemon centers.

The games don't have any information on it, though.
 
I don't believe we covered this already, but what happens to the pokemon that you defeat in the wild? In the games and anime(esp), when your pokemon faints or gets injured everyone starts flipping out that it needs to be healed and the whole "treat your pokemon well" theme. So let's say you are EV training on hordes with a level 100 tyranitar and are just destroying hordes upon hordes of weepinbell. What happens to those weepinbell? In the games when a pokemon faints it is, for all intensive purposes, dead until you use a revive or go to the pokemon center. So what happens to the masses of wild pokemon that you've been EV training on with tyranitar? Do they have a way of healing(reviving) on their own, and if so why don't the pokemon you own? Or do they all just die?
Like all life, Pokémon can heal on their own. They don't need a Pokémon Center or healing items (our requirement is more due to game mechanics). It just takes longer.

The real question is why can't we catch a Pokémon we've knocked out. The only thing I had is maybe something to do with how a Poké Ball works when it is catching the Pokémon, something to do with life signs, but it doesn't make sense since trainer owned Pokémon go back into their Poké Ball when knocked out.
This is the only explanation I have:
 
Yeah, honestly it makes MORE sense that you should be able to catch a pokemon when it's knocked out. And about pokemon healing, maybe pokeballs prevent natural healing. It would explain why in the games your captured pokemon don't heal over time.
 

Pikachu315111

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I don't believe we covered this already, but what happens to the pokemon that you defeat in the wild? In the games and anime(esp), when your pokemon faints or gets injured everyone starts flipping out that it needs to be healed and the whole "treat your pokemon well" theme. So let's say you are EV training on hordes with a level 100 tyranitar and are just destroying hordes upon hordes of weepinbell. What happens to those weepinbell? In the games when a pokemon faints it is, for all intensive purposes, dead until you use a revive or go to the pokemon center. So what happens to the masses of wild pokemon that you've been EV training on with tyranitar? Do they have a way of healing(reviving) on their own, and if so why don't the pokemon you own? Or do they all just die?
Hmm... maybe there's a difference between knocking out/fainting a Pokemon in a trainer battle and in a wild battle. In a trainer battle your Pokemon battle each other until they or their opponent pass out/fall into a sort of unconsciousness, forcing their trainer to return and heal it. Meanwhile in a wild battle remember the reason you're battling is because the Pokemon is testing your strength (well, at least according to lore). When you "knock out/faint" a wild Pokemon you're only making the Pokemon nearly pass out/lose consciousness. Upon reaching 0 HP the wild Pokemon had enough and submits with a defeat pose (letting your Pokemon know that it has won) and quickly runs off before the trainer has time to react like throw a Poke Ball. After running off the Wild Pokemon will naturally heal any wounds they would have gotten (maybe a bit longer than it would if taken to a Pokemon Center, but you know what they say: "time heals all wounds").

It would also explain why in the anime they treat an unconscious wild Pokemon seriously. They're not suppose to be unconscious, if a wild Pokemon had enough they're suppose to run away before things got extreme.

It's a shaky theory I'll admit, but otherwise I have to agree with Vader_the_White.
 
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I don't believe we covered this already, but what happens to the pokemon that you defeat in the wild? In the games and anime(esp), when your pokemon faints or gets injured everyone starts flipping out that it needs to be healed and the whole "treat your pokemon well" theme. So let's say you are EV training on hordes with a level 100 tyranitar and are just destroying hordes upon hordes of weepinbell. What happens to those weepinbell? In the games when a pokemon faints it is, for all intensive purposes, dead until you use a revive or go to the pokemon center. So what happens to the masses of wild pokemon that you've been EV training on with tyranitar? Do they have a way of healing(reviving) on their own, and if so why don't the pokemon you own? Or do they all just die?
Lets use a real life example. Suppose two lions were fighting each other. Food, rule over the pride the reason isn't important. Unless its a fight to the death most of the times one comes out the winner and the other is left to lick his wounds. I'd argue that's probably what pokemon that faint do. Considering the RNG mixes up stats everytime you encounter a pokemon its likely you aren't going to see the same pokemon Unless you happen to recognize the distinct pattern of a Spinda you fought
 

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New, slightly unconventional, umm... theory:

Very mild Delta Episode spoilers for ORAS follow.


I think somebody at the Mossdeep Space Center ripped off Norman. He bought tickets to watch the Litleonid meteorite shower at the space center with his wife, but has to pass them on to Brendan and May because work gets in the way. Some shenanigans do follow, but in the end the world is saved without the average Hoennite ever getting to know it was in danger, and there's plenty of time to sit down and watch the shower later, as Brendan and May is seen doing.

However, there are nobody else in the room.

Just how many people bothered to shell out for those tickets, again? I mean, the event is clearly announced beforehand, and the operation of the Space Center doesn't seem to be impeded by Team Aqua/Magma's intrusion - the regular visitors are back in place as soon as they are dealt with. The windows also look like they need washing, by the glimpse you get of the room. I'd have imagined it'd be much better to see the meteorites from outside the building, or places far from cities such as Mt. Pyre, Ever Grande City or the beach of Dewford. Either, Norman deserves his money back, or he deserves to pay double for buying such crappy tickets.
 

Pikachu315111

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Codraroll:
I found that odd too. When it was said that Norman had purchased tickets I thought to myself "What? why do you need to purchase tickets to watch a meteorite fly through the sky? Shouldn't anyone in Hoenn be able to see the meteorite if they know where to look?". I of course shrugged it off as I than noticed that the player's parents seem to have a dysfunctional marriage.

I can't really think up of a logical in-universe reason why they would need tickets (it would be one thing if Norman was just absent-minded and he did get duped, but the player's mother acts like the tickets were required and she's the one who wanted to go to the event so she would probably know if there weren't suppose to be tickets). I suppose you could say it was for atmosphere, the scene is meant to be a bonding (and possibly romantic) moment between Branden and May thus the scene was only made using them and not thinking "well there should also be a few random NPC here and there to make it feel more real".
 
So, I read through the various theories on this thread, some very interesting stuff being mentioned. I've got some points I want to bring up regarding theories I've been reading throughout.

Arceus's "Omnipotence": I always interpreted the information about Arceus to indicate that he was indeed very powerful, but the degree might have been distorted by Sinnoh folklore. I took Arceus to be the creature that created Sinnoh in their folklore, the same way Christians believe in a different god being responsible for creating the Universe than Japan's Shinto religion, for example. While incredibly trippy, the sequence at Sinjoh ruins only results in one of the Dragons, which I can more than accept Arceus could create himself. I understand bringing in the mechanics can be odd territory, but that hasn't stopped us before.

First, consider Unova. Kyurem's forms from absorbing either other Dragon reaches a BST of 700, 20 points above the power of either dragon, 40 above Kyurem's. Theoretically, this would mean recombining into the original dragon would make it 720-740, either the same as or more powerful than Arceus in terms of raw strength. Also, Kyurem, the empty shell after Zekrom and Reshiram split out, is only slightly weaker than Arceus's creations in the form of the Space-Time trio, Zekrom and Reshiram on par. I always took the "Original" Dragon to be a Pokemon of similar power to Arceus, worshipped in Unova the same way Arceus was in Sinnoh.

The other reason I say this pertains to Unova. The Weather Trio all have their "new" forms in Primal Reversions or a Mega evolution, all of which are significantly stronger than Arceus. Unlike most Megas, the Primal Reversions are treated as the "true" forms of these Pokemon, and their previously known incarnations as some restricted or incomplete power. What these tell me is that Gamefreak evidently isn't putting Arceus on that same pedestal he had in Gen 4, because for the remake, these 3 probably could've retained their base forms with little consequence to the plot: Groudon/Kyogre proceeds as normal, and Zinnia's ploy with them is still to make Rayquaza appear, unconnected to its Mega Evolution. Rayquaza in ORAS was also established as being worshipped by the Draconids, but unlike Arceus (who was in the Gen where lore started being a thing) and the Tao Dragon (who is never directly seen), Rayquaza does not display any outright mystical abilities, merely being extremely powerful. I could accept the idea of base Rayquaza being strong enough to destroy that Meteorite, in part because I played Mystery Dungeon where the issue with that feat wasn't "can I manage?" but "you all (the player party) will be caught in the blast".
Side note: Movie 12 depicts Arceus saving Poke-Earth from a Meteor and nearly dying as a result (save for Damos intervening). And this was in a context where it still curbstomped Dialga, Palkia, and Giratina simultaneously, so if anything the anime makes it seem more OP outside that context.

Mewtwo's Origins and Mega Stones: Now here's a bit of a trickier one. My best guess is that the scientists, possibly Team Rocket, were actually creating more than one Mewtwo, having worked with Fuji on the first one which was actually born of Mew. After this one's birth (which I'll refer to as Mewtwo-Prime for differentiating), Team Rocket took a sample of its DNA and attempted to clone another one, all the while conducting experiments to study the powers of Mewtwo-Prime. Unaware of its true powers, Mewtwo-Prime eventually in an emotional fit/fear destroyed the lab and fled. Born with the mind of an infant Mew and subjected to horrible experiments, it eventually found itself in Kalos' Pokemon Village, a refuge for Pokemon in hiding from humans. Mewtwo-Prime hid in the Unknown Dungeon, a particularly out of the way area, to completely isolate itself from humans: its expression seemed somewhat somber and its stance seemed defensive, like it was trying to scare the player off.

Meanwhile, Dr. Fuji, having seen what the scientists did to Mewtwo-Prime, he helped the actual Mew escape (Faraway Island) and settled in Lavender Town, taking on his life raising orphaned Pokemon as a way to atone for what he was part of. Meanwhile, Team Rocket was in the process of attempting to clone another Mewtwo (even the anime notes in Return of Mewtwo that, while inconvenient, they could clone it again in years), but wanted to make it more battle-minded (hence the Berserk Gene in the original Gen 2 games). This Mewtwo became too battle hungry, however, and thus secluded itself in the Cerulean Cave, home to the strongest (wild) Pokemon in Kanto, which also explains why, despite its power, it stayed in the cave. From here, proceed with other fan theories about Team Rocket seeking the Master Ball or Ghost Pokemon to recapture Mewtwo, choosing to recapture this one since they didn't know Mewtwo-Prime's location, Fuji obviously wanted Mew hidden, and they now lacked anything from which to clone another Mewtwo.

As for the Mega Stones, it overlaps with a theory I have on them: The Mega Stones for one Pokemon are not identical. There is not one specific composition for Venusaurite, but rather a stone that yields such an effect being a Venusaurite. Mega Stones are just rare stones that happen to react with a Pokemon to induce Mega Evolution, but without consistent traits beyond that, hence why the stones can't be mass produced (from anything I've seen). Branching stones are just two stones reacting with a Pokemon, but in slightly different manners, hence the X and Y forms. So Mewtwo's Mega Stone doesn't require Mewtwo to be a natural Pokemon, it just means a stone exists somewhere that happens to react with Mewtwo to induce Mega Evolution. Being next to it in the UD is convenient, but THAT much I can chalk up to suspension of disbelief.
Essentially, I think of the Mega Stones a bit similar to Deoxys and the Meteorites: They're not all directly identical, but they react similarly enough to produce the same effect (Deoxys' forme changes or a Pokemon's Mega Evolution), which I think makes further sense if you think of the Mega Evolutions as very powerful formes (Rotom and Kyurem to an extent already offering precedence for Formes increasing stats beyond simply redistributing them).


Marowak and the Electric Weapon: I always assumed the electricity used by Pokemon in battle is not on the same level as what people would employ for weapons. Remember, most Pokemon don't tend to be using their electricity lethally, but either to exhaust/tranquilize the opponent, or stun them (in the case of something like Thunder Wave). For an anime comparison, the Zoroark movie is what I think of. Despite Pikachu's electric attacks being present so often, Zoroark's cage and Kodai's wrist shocker are NOT treated as just annoyance: Zorua is shown in genuine pain, the cage take Zoroark going Mama Bear to push past the shocks and break out of, and that claw KILLS her by the time things end. Kodai is shown not to care for Pokemon or anyone, so I wouldn't put it above him to use something that could generate lethal amounts of electricity. The anime explanation for Grass and such Pokemon resisting Electric attacks is that they defuse it into the ground. However, that still does require the electricity to pass through them, just usually not long enough to do lasting damage (Treecko flinched form Thunderbolt, but wasn't visibly damaged by it on the ground). Theoretically, passing a electricity through them continuously could still inflict harm, since even if they defuse it, there's still a constant stream of energy in their body. Barring that, blunt force from the Baton itself might have simply cracked Marowak's skull, which would allow the current into a part of the body it's not normally geared to protect (similar to how cuts or fractures make the area more prone to infection since it's not normally exposed).
 
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So, I read through the various theories on this thread, some very interesting stuff being mentioned. I've got some points I want to bring up regarding theories I've been reading throughout.

Arceus's "Omnipotence": I always interpreted the information about Arceus to indicate that he was indeed very powerful, but the degree might have been distorted by Sinnoh folklore. I took Arceus to be the creature that created Sinnoh in their folklore, the same way Christians believe in a different god being responsible for creating the Universe than Japan's Shinto religion, for example. While incredibly trippy, the sequence at Sinjoh ruins only results in one of the Dragons, which I can more than accept Arceus could create himself. I understand bringing in the mechanics can be odd territory, but that hasn't stopped us before.

First, consider Unova. Kyurem's forms from absorbing either other Dragon reaches a BST of 700, 20 points above the power of either dragon, 40 above Kyurem's. Theoretically, this would mean recombining into the original dragon would make it 720-740, either the same as or more powerful than Arceus in terms of raw strength. Also, Kyurem, the empty shell after Zekrom and Reshiram split out, is only slightly weaker than Arceus's creations in the form of the Space-Time trio, Zekrom and Reshiram on par. I always took the "Original" Dragon to be a Pokemon of similar power to Arceus, worshipped in Unova the same way Arceus was in Sinnoh.

The other reason I say this pertains to Unova. The Weather Trio all have their "new" forms in Primal Reversions or a Mega evolution, all of which are significantly stronger than Arceus. Unlike most Megas, the Primal Reversions are treated as the "true" forms of these Pokemon, and their previously known incarnations as some restricted or incomplete power. What these tell me is that Gamefreak evidently isn't putting Arceus on that same pedestal he had in Gen 4, because for the remake, these 3 probably could've retained their base forms with little consequence to the plot: Groudon/Kyogre proceeds as normal, and Zinnia's ploy with them is still to make Rayquaza appear, unconnected to its Mega Evolution. Rayquaza in ORAS was also established as being worshipped by the Draconids, but unlike Arceus (who was in the Gen where lore started being a thing) and the Tao Dragon (who is never directly seen), Rayquaza does not display any outright mystical abilities, merely being extremely powerful. I could accept the idea of base Rayquaza being strong enough to destroy that Meteorite, in part because I played Mystery Dungeon where the issue with that feat wasn't "can I manage?" but "you all (the player party) will be caught in the blast".
Don't forget, the Sinnoh we've seen is in a different time-line to ORAS, meaning Primal Groudon and Kyogre might not have existed in that reality (or realities since there are three different versions of events thanks to multiple villainous teams), so the relative power of Arceus might be stronger. Who knows what might happens by the time we get to the virtually inevitable Diamond and Pearl remakes in about 4-5 years.
Also, ancient inhabitants of Sinnoh might have had little to no interaction with ancient Hoenn inhabitants, so they likely didn't have knowledge of the weather trio, so Arceus may still be the most powerful Pokémon they knew about. And I doubt most NPCs know about BST.
Also, great explanation about Mega Stones.
 
Don't forget, the Sinnoh we've seen is in a different time-line to ORAS, meaning Primal Groudon and Kyogre might not have existed in that reality (or realities since there are three different versions of events thanks to multiple villainous teams), so the relative power of Arceus might be stronger. Who knows what might happens by the time we get to the virtually inevitable Diamond and Pearl remakes in about 4-5 years.
Also, ancient inhabitants of Sinnoh might have had little to no interaction with ancient Hoenn inhabitants, so they likely didn't have knowledge of the weather trio, so Arceus may still be the most powerful Pokémon they knew about. And I doubt most NPCs know about BST.
Also, great explanation about Mega Stones.
Like I said, I do chalk up the worship of Arceus to it just being the most powerful Pokemon they knew about, similar to Unova perhaps only knowing the original Tao Trio dragon.

And I took the BST ideas to be more just a way of evaluating how Gamefreak wanted us to view the Pokemon. For example, Regigigas may not be nearly as effective as other Legendaries with his BST, but him being given those numbers is Gamefreak's way of indicating "within the game world, this is a very powerful Pokemon." I just take the Primal Reversions vs Arceus thing to be a way of saying "as of everything available right now, these Pokemon are probably stronger relative to Arceus." If the Gen 4 remakes introduce some kind of "Creator Arceus" form with Base 820 stats of some kind, then I'll believe they do indeed want Arceus to be seen as some kind of supreme deity.

That said, considering how soon they introduced Pokemon close to and then surpassing Arceus in terms of gameplay power, I think it may be Gamefreak trying to work around writing themselves into a corner with the lore, considering its unmatched 720 BST indicates they wanted Arceus to be this powerful not just from a lore perspective, but reflected in the gameplay. I recall a parody video where Dawn and Lucas basically go over all the Legendaries, realize they had God, and Gamefreak has nothing for the 5th gen. Introducing other Olympus mons intended to be as/more powerful than Arceus knocks him down from "Supreme all powerful" to being among a crowd of worshiped Olympus Mons, since nerfing Arceus's stats would probably just screw with things more than necessary.
 
I honestly see the Sinnoh folks witnessing rainbow llama once then called it a god, I don't know I just can see an interdimensional creature as a true God after going full lovecraftian reading spree. They always looked to me as interdimensional fauna that awed the plebians.
 
I honestly see the Sinnoh folks witnessing rainbow llama once then called it a god, I don't know I just can see an interdimensional creature as a true God after going full lovecraftian reading spree. They always looked to me as interdimensional fauna that awed the plebians.
That is something we need to consider: misidentification by ancient people. I mean, we got the cyclops from elephant skulls. Hell, we as a species are still likely doing it considering theories about ancient spacemen just because ancient carvings look vaguely like spacesuits.
Also, this is likely Mega Arceus:
 
That is something we need to consider: misidentification by ancient people. I mean, we got the cyclops from elephant skulls. Hell, we as a species are still likely doing it considering theories about ancient spacemen just because ancient carvings look vaguely like spacesuits.
Also, this is likely Mega Arceus:
If we go by nico nico take on llama drama we could call this official.
 
Nah, stories about legendaries in this series have pretty much all turned out to be true, and that Arceus event which took place in Gen IV unlocked some new side content which pretty much collaborated the stories, my favourite being the hiker who appears first at the Oreburgh mines, than at Canalave Library. I think it's the same hiker who shows up in Johto in HGSS.

Anyway, anyone who's been closely following the build up to the Hoopa movie will probably have realised by now that it's an Arceus movie in disguise. The main movie exclusive characters all have a special necklace shaped like the Arceus Ring, the special pre-order Ticket Event is Arceus instead of Hoopa like you'd expect it to be, and in the trailer, what at first glance looked liked Arceus' Judgment animation, actually looks likes the beginning of a transformation animation.

It really couldn't be more obvious, Arceus is going to get his divine form in the movie and save the day, and those clever people who pre order will get to use it in the next Pokemon game. In one fell swoop Arceus has the highest BST again, not that it matters Tbh.
 

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Almighty Arceus:
Well personally I never saw Arceus giving the player access to its full power. Actually Norne brings up Lovecratfian lore and that has something about its eldritch abominations (EA) creatures which I think would perfectly fit with Arceus. A big thing about Lovecraftian lore is that the EA aren't what anyone can "see" of them (or at least see without going insane, but that's beyond the point). The EA are essentially formless having more than just the 3 spacial dimensions of height, length, and width. Infact some of them create an avatar they control like a puppet which mortals can see without going insane and at the same time the EA can channel its power through to do what they want. And I think (or at least like to think) that's what Arceus is, a formless and infinitely powerful EA who has created an avatar which it channels a tiny bit of its power through to communicate with us mortals.
Why does Arceus let the player catch its mortal avatar? The player has proven themselves as an intriguing person who's able to form incredibly strong bonds with Arceus's children, the Pokemon species. It wants to observe the player and entices them to let the player catch it by giving them use the power which Arcues has initially given its avatar (and if need be Arceus can further limit or strengthen the avatar's power). Being its just an avatar the true Arceus is free to do what it needs to, the player is still a human so only has about a century to live which comparatively to Arceus is just a blink of the eye (if even that long), and finally Arceus can probably create a new avatar if it needs something done down at that level. That could also explain why Arceus only creates one of the Spacetime Dragon for the player in HGSS, it wanted to present the unique character with a gift that it could do so using the power of the pedestal in the Sinjoh Ruins, but only one because they don't want to make the player too powerful (I always took what Arcues was doing in that event as it using the pedestal's power to create and then destroy a micro universe so that it could create another spacetime dragon without it having it chained down to a universe (and maybe showing off its power, oh, and also what sort of forces generally goes into making a Pokemon egg)).
Why is Arceus's avatar BST just 720? Well at the time it created the avatar it was the most powerful Pokemon we've ever seen and still is for non-Mega Pokemon (which as Vader_the_White pointed out is another timeline, but we'll get to that). As for the Unova Original Dragon being as strong as Arcues, I imagine that's a special circumstance or maybe even an experiment on Arceus's part to allow a Pokemon use the boundless power that comes from human ambitions (though it probably didn't see it splitting itself apart, but hey that's what experiments are for). At most I would say maybe Arceus allowed/capped the Unova Original Dragon's power at 720 because it was still skeptical it mortals could take a physical being with any more power.
What about the Arceus avatar in the Mega Universe? When the Sinnoh remakes come around I can't see how they'll give up a chance to give Arcues, or rather the Arceus avatar, a Mega Evolution. I'd imagine its basically the player unleashing ALL the power that Arceus had put into its avatar though since its a temporary power-up and other Pokemon are given access to this power (and making some stronger than Arceus) it'll allow that so once again it could be the strongest Pokemon (BST of 820); it could also be an experiment on Arceus's part to see if mortals could take physical beings with much higher power.
But if Arceus is so powerful what about people worshiping Rayquaza, it being taken out by a meteor, etc.? For the worship of other deity-like Pokemon that's probably people just being people. The Draconians worshiped Rayquaza because it save them and all of Hoenn by using the power of the people's prayers, thus the people not only say it as a powerful Pokemon but also as "part of" Rayquaza as they can help it achieve even more power. The Unova Original Dragon used the power of human ambitions which was eventually split into Reshiram's "Truth" and Zekrom's "Ideal" so once again people feel a strong connection to it. As for the people of Sinnoh, only they seem to worship Arceus because that's where Arceus first set up shop so its where there's the most evidence of "Arceus" as well as its first few creations (the Spacetime Dragons and the Lake Gaurdians). People not only worship what's the most powerful thing they know of but also what they feel they have a closer relationship to, just because its revealed another region has a creature just as strong or stronger doesn't mean they'll just drop their religion and start worshiping the new stronger one.
Also remember the anime isn't made by the exact same people who make the games. As pika pal pointed out, its taken out by a meteor yet can take on all 3 Spacetime Dragons? I suppose if you put in my theory into effect that maybe at that time the Arcues avatar underestimated the meteor's strength and ended up badly injuring itself. It was dying, though had it died the actual Arceus could have just created another one but luckily Damos saved it. Flash forward to the Arceus avatar waking up after having been betrayed, Arceus is P1$$3D and so is no longer holding back. Its unleashing ALL its power so it can easily take on the Spacetime Dragons.

Mewtwo's Origin:
Hmm, while I wouldn't say other Mewtwo weren't made I think only one was made in Kanto by Dr. Fuji. How I see it, an organization (be it Team Rocket or another) decided they wanted THE (one) ultimate Pokemon so got a group of scientist together to do so, one being Dr. Fuji who I'm guessing from his importance in the story probably was the lead scientist. Deciding to base it on Mew who's DNA is easily manipulable, they find a piece of Mew DNA (probably on Faraway Island, thus why the sign was written by Mr. Fuji) and started work on cloning their ultimate weapon. They succeed but it was too powerful and it escaped (going to Cerulean Cave/Kanto's Unknown Dungeon), after so the scientists disbanded. Now we know that Dr. Fuji probably retired after the incident, probably feeling horrible they made such a destructive Pokemon, and went to Lavendar Town and started running the Volunteer Pokemon House. But what about the other scientists? I wouldn't be surprised if some of them probably were shady and went to work for other organizations with the promise of making them their own ultimate Pokemon (probably also having a bit of Mew's/Mewtwo's DNA and data on the creation process). Obviously there is still a limited about of Mewtwo, kind of defeats the purpose of an "ultimate" weapon to have a lot of them running around, but that would explain why there are Mewtwo elsewhere.
I also standby my theory that, though incredibly rare and probably non-existent, there is such a thing as a natural Mewtwo. Mew was created probably by Arceus to populate the Pokemon World with a variety of species which Mew would evolve into (thus why Mew had DNA of "every" Pokemon, in actuality every Pokemon has DNA from a Mew). Depending on the environment Mew evolved into Pokemon species that would thrive there. This was when the Pokemon World as first forming, nowadays the world is filled with Pokemon and the Mew who are left no longer need to evolve into other Pokemon. However they still have that trigger inside of them and I wouldn't be surprised if that trigger could activate due to a flaw or accident and the Mew, now evolving without any environmental stimulus to shape its evolution, evolves like a Pokemon would into a stronger form of itself: Mewtwo. Of course being how rare Mew is and this would be a rare condition it probably hasn't happened more than once. Why do I say once? Because in Pokemon Ranger: Guardian Signs (which is canon like all other Pokemon Ranger games) there is a Mewtwo who was in hyperbolic sleep on board the Dark Fortress and I think it was said by the Sociatea it was there when the got there (and being the last time the Dark Fortress was used in ancient times before modern science, that would mean either a natural Mewtwo existed in ancient times or maybe a Mew was put in there and over the years in hibernation the evolution triggered and it became a Mewtwo).

Mega Stone Origins:
However I do agree with you on the Mega Stones. Mega Stones are just stones which just so happen to match certain Pokemon's signature/essence/aura/wavelength/whatever and that Pokemon can use it to Mega Evolve. The stones weren't specially made for the Pokemon, the stone was just radiated with Infinity Energy (the energy that the Ultimate Weapon used and later Mr. Stone was able to replicate). And it just so happens there are stones which react to Mewtwo. I suppose it could also be possible over time the Mega Stones could absorb the essence of Pokemon living and change so they become Mega Stones for that Pokemon, so maybe there wasn't Mega Stones for Mewtwo originally but when some came into existence a few stones were effected by them and eventually changed into Mewtwonites.
 
So, I have noticed that Kanto is the only region of the first six that has a science fiction theme to it, due to its genetics motif, while the rest have some sort of fantasy theme to them, starting from Johto and its mythology motif, but doesn't really become noticeable until Unova with the Dream World and whatnot, alongside interaction between opposites. Is this just a case of Early-Installment Weirdness?
 

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So, I have noticed that Kanto is the only region of the first six that has a science fiction theme to it, due to its genetics motif, while the rest have some sort of fantasy theme to them, starting from Johto and its mythology motif, but doesn't really become noticeable until Unova with the Dream World and whatnot, alongside interaction between opposites. Is this just a case of Early-Installment Weirdness?
Um, what about Gen IV? Team Galactic had a strong science fiction theme (true there plan do involve gods of time and space, but they do go about their plans in a sort of science fiction-y way).

Hmm, let's go over the themes of each gen:

Kanto: Honestly I wouldn't say it a has a singular theme, if any. Kanto feels the most "normal" since, being the first game, they wanted players to get immersed. Making the world feel normal helps you get into it more with the elemental monsters justifying non-normal things like letting kids go on a cross region journey where they fight bad guys and become the strongest trainer ever. Speaking of the bad guys, they too feel normal just being a group of thugs and later turn into the yakuza/mafia. They're just criminals trying to make a profit, no plan to take over the world or using the elemental monsters to do magical stuff. That said, there is still other themes in there to add variety. Pokemon themselves feel mystical, Lavender Town and Pokemon Tower brings in some horror, this world has martial artists and ninjas, and areas like the Pokemon Mansion, Power Plant, and Unknown Dungeon brings in an air of mystery. Of course many games have segments like those, but due to Kanto having no theme these set pieces remain longer in your mind as they're something to latch onto. I would call Kanto's theme "Introduction", since its meant to introduce you into the world of Pokemon
Johto: Johto's theme is more heavily influenced by myths and legends. While Gen I's Legendary have little to no back story, every Legendary in Gen II has backstory and its somewhat prevelant (with these being the first games to have Legendaries as the version mascots). In addition Johto felt like an expansion on the Pokemon world. Not only is there new Pokemon and a new region, the villains are a not fragmented Team Rocket, you later discover the Pokemon League is the same place with some of the same people as the first game, and you can go through Kanto and see what changes happened there. I would call Johto's theme "Expansion", as it not only expand upon older ideas but feels like a direct continuation of what you did in the last game.
Hoenn: Hoenn's initial theme is the balance of nature, being the first (and only game) to have two villains both who are eco-terrorists wanting to change the environment believing to make a better world. It has a heavy nature theme with many kinds of environments (forest, caves, desert, beach, seas (so many water routes), island, volcanic (which you could say also felt a bit like a snowy area due to the falling ash)) and many of the big dungeons being caves. This point in further emphasized with New Mauville in the original games and Mauville City itself in ORAS, which is more technological and high tech then almost every where else. Hoenn's theme is "Environment", not only are the villains eco-terrorists and there are many natural places but also the updated graphics of the GBA let them do more with the environment like have reflections in the water, footprints in the sand, overworld weather effects, and just able to make more detailed sprites and animations.
Sinnoh: Sinnoh's theme was very space related. Team Galactic want to use space gods to rewrite the universe (though oddly enough it was Hoenn to be the first game to let the character go into space). This game would be approved by Space Core. Anyway, there's also a science fiction feel as well, Team Galactic don't only look like they're from space but they use technology do about their plan (using the Galactic Bombs to empty lakes, creating the Red Chain to control the Spacetime Dragons, their bases are labs with all sort of technology strewn about). Also it feels like they try to "explain" things, like how Mt. Coronet has a magnetic field which lets some Pokemon evolve, the region being split in two has made the Shellos family look different depending what side they're from, there's the Moss and Icy Stone that gives off radiation to let Eevee evolve, etc.. Also the Distortion World feels like a very science fiction place. Sinnoh's theme is "Advancement", not only referring to the games sci-fi feel but also to the games themselves using 3D models in the overworld and the game's storyline having advanced so much you literally encounter GOD. Where to go from here?
Unova: Unova tries to blend the simplicity of the Gameboy days with the complication of recent games. I'll just reveal Unova's theme right here and now, its "Philosophy". Truth and ideals, ideals an truths, get used to those two words (or three if you count "and") because this is the first Pokemon games to have a heavier focus on the story and is of philosophical ideas, mainly to do with Pokemon. Is it right for people to use Pokemon? Should people and Pokemon be even living together? What is the bond between people and Pokemon? Is it better to seek out the truth or follow ideals? What if you don't like the truth or your ideals are unaccomplishable?... I DON'T KNOW! All I want to do is catch colorful creatures and have them fling elemental attacks at one another! Even the game design questions some of the choices that were made with it. Was it right to exclude old Pokemon in the game? Did adding them back into the sequel make anything better? Was making the path linear too restricting? Was the sequel having you jump around the map make it feel disjointed and the map kind of useless? Should the bad guys have a point about using Pokemon to fight or should the big bad be a manipulating sociopath thus making the villain's ethical question moot? Lots and lots of philosophy, but not many answers because in the end they were essentially asking hypothetical and were experimenting with the Pokemon formula to see what worked and didn't work.

I'm going to hold off on commenting on Kalos's theme until its over. If I was forced to name a theme at the moment I would say "Mortality", the Legendary are incarnations of Life and Death Destruction, the villains want to kill everyone and make themselves immortal, one of the characters IS immortal and killed a lot of people and Pokemon, and there's a lot of talk about living life to the fullest and making memories, experiencing things, and becoming the best that you can be (a possible allusion to also the Mega Stones). But who knows what XY2 will bring and can possibly change this theme.
 

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