SPOILERS! Mysteries and Conspiracies of Pokemon

Here it is! I used WaffleTitan's index to create a master one, which hopefully a mod can put on the first page. I decided not to use links for the pages, because it's so easy to change pages without a link. I also added our new topics of Diancie and gradual evolution over time, and categories. I hope you all enjoy this! Sorry for the double spoiler, did something by mistake.


Index of Mysteries
as of
7/18/2015

Character Related
Ghost Girl
2, 14, 42, 43

AZ's Size and Age
4, 6, 42

Emma (X/Y)
9, 30

Lack of Father
6, 13, 14, 50

Pokemon Champion
17

Looker
18, 30, 42

ORAS Cameos
20

Norman
26, 27

Pheobe/Grandma
40, 43

N
24, 30, 45, 46, 47, 48

Pokemon, Pokemon Related, and Dex Busting
Pokedex Entries
1, 10, 27, 28, 33, 34, 35, 42, 47, 48

Original Pokemon
5, 6, 7, 23, 33, 35, 38, 39

Darkrai Killing a Girl
1, 43

Multiple Legendaries
4, 5, 23

Deoxys
8, 13, 18, 26, 36

Evolution
11, 12

Genesect
13, 31, 46, 48

Forces of Nature Trio
13

Malevolent Pokemon
15, 16, 17, 34

Mega Evolution
23, 24, 29, 33, 36, 37, 47

Kyogre and Groudon
24, 25, 34, 36, 37

Unown
31

Marowak's Death
32, 33, 43

Zygarde
37, 49, 50

Mewtwo
38, 41, 42

Starters
43

Ancient Pokemon
48, 49

Mysterious Pokemon
49, 50

Diancie
51


Gradual Evolution
51


The World and Technology
Breeding
2, 3, 5, 6, 12, 13, 23, 27, 31, 32, 39, 40, 41, 42

Multiverse
14, 15, 22, 23, 24, 25, 31, 36

Timeline
20, 21, 22, 23, 25, 28, 31, 40

Couriway Station
2

How is the Pokemon World Run
2, 19, 25, 26, 49

How do TMs Work
3, 4

Real Animals
4

Pokemon War
6, 43

Pokemon-Human Relation
6, 7, 34, 39

Stolen Submarine
7, 8

Tipping
8, 9

Mirage Island
9

Pokemon World Tournament
9, 10

Transportation
13, 32

Pokeball
13

Route 14 Story
14

Sea Mauville
16, 17, 27, 45

The Champion
17

Weather
20

Super Training
21, 22

Religion
26, 27

Strange
Occurrences
30, 36

Death
43, 44, 45, 46, 47

Pokemon as Food
3, 4, 35

Strange
Souvenir
12, 31, 50


Hey, just saying, we still should put this in on the first page of the thread. I think it would help a lot. If you are a mod, you should edit it on. Thanks.
 

Pikachu315111

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Pretty much most of Italy's politics since 1950. Ask yourself why Giovanni has an italian name.
Because outside of Japan they made Team Rocket into a mafia organization (they're actually based on the Yakuza).

New Mystery: Over on the Unpopular Opinion thread we got to talking about Zinnia and during our conversation I just realized something: Why did Zinnia bring the player to Sky Pillar. Now being the Champion I guess she figured she couldn't just steal our Key Stone without getting trounced (then again she had no qualms attacking people and I doubt the player could take Zinnia on person-to-person, especially if she did a sneak attack... actually she did knock us out on Sky Pillar!), but why did she drag the player into all this? At no point did Zinnia rely on the player to do something for her, up till she failed to Mega Evolve Rayquaza she was doing everything on her own. I could only conclude he brought us up so we could use our Key Stone along with the 5 she had to help summon Rayquaza, but if that wa a case why didn't she also bring Steven? Even if she for no reason didn't like him he still had a Key Stone and wouldn't 7 Key Stones be better than 6 (she was only going off a hunch that the Key Stones would summon Rayquaza so wouldn't he want as many as possible?). And that's not even mentioning how she took an instant liking to the player for no reason besides the plot saying so. So to repeat the question, what was Zinnia's thinking for bringing the player to Sky Pillar?
 
Because outside of Japan they made Team Rocket into a mafia organization (they're actually based on the Yakuza).

New Mystery: Over on the Unpopular Opinion thread we got to talking about Zinnia and during our conversation I just realized something: Why did Zinnia bring the player to Sky Pillar. Now being the Champion I guess she figured she couldn't just steal our Key Stone without getting trounced (then again she had no qualms attacking people and I doubt the player could take Zinnia on person-to-person, especially if she did a sneak attack... actually she did knock us out on Sky Pillar!), but why did she drag the player into all this? At no point did Zinnia rely on the player to do something for her, up till she failed to Mega Evolve Rayquaza she was doing everything on her own. I could only conclude he brought us up so we could use our Key Stone along with the 5 she had to help summon Rayquaza, but if that wa a case why didn't she also bring Steven? Even if she for no reason didn't like him he still had a Key Stone and wouldn't 7 Key Stones be better than 6 (she was only going off a hunch that the Key Stones would summon Rayquaza so wouldn't he want as many as possible?). And that's not even mentioning how she took an instant liking to the player for no reason besides the plot saying so. So to repeat the question, what was Zinnia's thinking for bringing the player to Sky Pillar?
She is a baton pass sue, we gotta see her fail so we step up the game, also Steven was annoyed as fuck with her ramblings and wanted to stay in the control room to help if needed.
 
How about this idea. What if the reason we can so "easily" capture the embodiments of the raw forces of nature is because, yes they have power over those forces, but because there are others of their particular species hidden SOMEPLACE inaccessible to humans and normal Pokemon where they, even in slumber, regulate the status quo of balance while their conscious brothers can throw it out of whack (see ORAS). Like, if we take Dialga (Sinnoh Dialga) and kill it, time won't suddenly disappear. Partially because we have two confirmed canon Dialga (Sinnoh Dialga and Sinjoh Arceus born Dialga), but also perhaps due to a Dialga elsewhere maintaining status quo
 

Pikachu315111

Ranting & Raving!
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How about this idea. What if the reason we can so "easily" capture the embodiments of the raw forces of nature is because, yes they have power over those forces, but because there are others of their particular species hidden SOMEPLACE inaccessible to humans and normal Pokemon where they, even in slumber, regulate the status quo of balance while their conscious brothers can throw it out of whack (see ORAS). Like, if we take Dialga (Sinnoh Dialga) and kill it, time won't suddenly disappear. Partially because we have two confirmed canon Dialga (Sinnoh Dialga and Sinjoh Arceus born Dialga), but also perhaps due to a Dialga elsewhere maintaining status quo
We can easily capture the because we showed we're worthy of doing so and they decided to come along willingly. It's not like they can't maintain order while with us, Pokemon have had no problem in the past popping out of their Pokeball and I'm pretty sure that also goes for Legendaries. If there's something that needs them to maintain they can easily do so from the Pokeball, if there's something that needs their immediate attention they can come out of their Pokeball to address it. Finally thy probably plan on only being with you for a short while, eventually you'll either decide to release them once you're assumingly done traveling around or if you keep hold of them until you pass on (I doubt they'll let you give them to your kids or someone else, they can catch the Legendary themselves if they want it). So you can say Legendaries are on temporary loan.
 
Most likely it's just a planar being that has abilities that control such forces in our realm, who knows how many rainbow llamas where laying eggs in their interdimentional ecosystem before the dudes at Sinnoh started treating them as Gods in their myths.
 
I hate to say this, but I think the whole capturing legendaries is basically just a game mechanic. If you couldn't catch them it would majorly detract from the game. In real life, I don't thing legendaries would ever be captured.
 
I hate to say this, but I think the whole capturing legendaries is basically just a game mechanic. If you couldn't catch them it would majorly detract from the game. In real life, I don't thing legendaries would ever be captured.
Legendaries would just choose you if they thought you were worthy or could use them to advance their own agenda. They might feign a battle. Of course lesser legendaries might be beaten still and captured.
 

Cresselia~~

Junichi Masuda likes this!!
Because outside of Japan they made Team Rocket into a mafia organization (they're actually based on the Yakuza).
Are you sure that they are Yakuza?
I thought the gangsters on the streets in Unova with a Krookodile coat are the ones that are Yakuza instead.
Because that Krookodile embroidery reminds me of the dragon embroidery the Yakuza would have.
 

Pikachu315111

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Are you sure that they are Yakuza?
I thought the gangsters on the streets in Unova with a Krookodile coat are the ones that are Yakuza instead.
Because that Krookodile embroidery reminds me of the dragon embroidery the Yakuza would have.
Well now having done some looking around I think Team Rocket is probably just based on a criminal organization just in general. Associating them with one or another probably depends where you came from. If you're from Japan where the Yakuza are they probably seem more Yakuza-like, while in the US they seem more Mafia-like. In the end they're a criminal organization who's sole goal is to exploit others to get as much money and power that they can.

As for the Roughnecks in Unova, that is a bit of a carried over. Previous Roughnecks had a Gyarados on their back (Gen IV) so when they brought them back for Gen V they put a Krookodile on their back since it was a new Pokemon that looked ferocious and was a reptilian Dark-type. While associating yourself with an animal is a multi-cultural thing, having said animal woven on the back of your clothes does seem a more Asian thing in my memory. However such an idea has spread throughout the world so while Asian in origin it's not Asian exclusive. Also Unova is based on New York which is a cultural melting pot, GF even said they based several things in Unova off other places around the world (best example are the Starters. Oshawott was given a Japanese feel, Snivy a European feel, and Tepig a Chinese feel).
 
Also Unova is based on New York which is a cultural melting pot, GF even said they based several things in Unova off other places around the world (best example are the Starters. Oshawott was given a Japanese feel, Snivy a European feel, and Tepig a Chinese feel).
Huh, that seems obvious but I never really caught on to that. Although that makes it both more like New York, being the great American melting pot.

Or so School House Rock used to tell me.

Sorry to bring up the Cat's in the Cradle mystery again, but I had some thoughts about the disappeared Dads that haven't quite been mentioned yet. Or they have been and I missed them in my archive binge.
*Edit: Yep, Darth Manaphy already talked about point #1.

1. Kalos-Dad: He's mentioned at least twice, once if you investigate the computer in your room (saying it's a gift from him) and another time with your mom regarding her past as a Rhyhorn Racer in the post-game. Given that your family recently moved and Grace (your mom) seems both fond of your father but says somewhat flirtatious remarks regarding Sycamore, I think this is the only father that's probably dead (or had a very squeaky clean divorce). Given these two odd references where the other Dads besides Norman are (almost) completely unmentioned, I think your mom and you moved to Kalos after his passing (or divorce) for some space and a fresh start. At least, that's my take on it.

2. Family dynamics in the Pokemon universe are just weird. While we talk a lot about parental abandonment from the child's perspective, let's look at it from your mom and dad's. One day their child gets a pokemon and then up and leaves at the rip 'ol age of 10 to 13ish. To hardly ever visit or call. Heck, in canon the two sequel games (Gold/Silver and B2W2) the previous moms directly mention that the previous protagonist left on a journey and hasn't made any contact since. Both also mention being both extremely worried for them but also rather nonchalant about it. Even if your dad did visit, would you even be around to see him? Makes me think that pokemon trainer is just this accepted career path where you are expected to spend months to years on the road away from family, and despite occasional misgivings everyone is cool with it. So it's likely that your disappeared dads are pokemon trainers on their own journeys, and their absence is considered natural in-universe (if parental/spousal neglect in reality).

Plus considering how much cash you can rake in for beating up the pokemon of small children, can you blame them for settling on this career choice?
 
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Pikachu315111

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Huh, that seems obvious but I never really caught on to that. Although that makes it both more like New York, being the great American melting pot.

Or so School House Rock used to tell me.

Sorry to bring up the Cat's in the Cradle mystery again, but I had some thoughts about the disappeared Dads that haven't quite been mentioned yet. Or they have been and I missed them in my archive binge.
*Edit: Yep, Darth Manaphy already talked about point #1.

1. Kalos-Dad: He's mentioned at least twice, once if you investigate the computer in your room (saying it's a gift from him) and another time with your mom regarding her past as a Rhyhorn Racer in the post-game. Given that your family recently moved and Grace (your mom) seems both fond of your father but says somewhat flirtatious remarks regarding Sycamore, I think this is the only father that's probably dead (or had a very squeaky clean divorce). Given these two odd references where the other Dads besides Norman are (almost) completely unmentioned, I think your mom and you moved to Kalos after his passing (or divorce) for some space and a fresh start. At least, that's my take on it.

2. Family dynamics in the Pokemon universe are just weird. While we talk a lot about parental abandonment from the child's perspective, let's look at it from your mom and dad's. One day their child gets a pokemon and then up and leaves at the rip 'ol age of 10 to 13ish. To hardly ever visit or call. Heck, in canon the two sequel games (Gold/Silver and B2W2) the previous moms directly mention that the previous protagonist left on a journey and hasn't made any contact since. Both also mention being both extremely worried for them but also rather nonchalant about it. Even if your dad did visit, would you even be around to see him? Makes me think that pokemon trainer is just this accepted career path where you are expected to spend months to years on the road away from family, and despite occasional misgivings everyone is cool with it. So it's likely that your disappeared dads are pokemon trainers on their own journeys, and their absence is considered natural in-universe (if parental/spousal neglect in reality).

Plus considering how much cash you can rake in for beating up the pokemon of small children, can you blame them for settling on this career choice?
A Sycamore Romance: I just want to point out that the thing between your mom and Sycamore is actually completely fanon. Sycamore never sent your mom a love letter, it was the letter asking if he could have her child help him by going on a Pokemon journey. Your mom didn't give any indication she wanted Sycamore, I always took the "love letter" comment as her just joking around and impressed with very nice handwriting.
Now this point doesn't really have anything to do with your dad, but I think its something people like to take out of context which is alright but my problem starts when they treat it as canon. To be honest Sycamore seems more interested in you than your mother (don't you dare take that the wrong way, you perfectly know what I mean. Actually that brings up another question...).

New Mystery: 5 Kids, 3 Starters
So Sycamore asked 5 kids to have them do his field work: Calem, Serena, Shauna, Tierno, & Trevor. Now obviously these kids are going to need Pokemon so Sycamore sends them a set of starters... a set of 3 Pokemon. What? Also why was it decided that it would be your rival and Shauna who would get the other two Starters? Did Tierno and Trevor already have Pokemon? Okay, if they did fair enough, but then comes the time Sycamore gives out the Kanto Starters. Well being Calem, Serena, and Shauna got the Kalos Starters it would only be fair for Tierno and Trevor to get the Kanto Starters (the player also getting one because you're the player, if the needed a reason maybe its because you're the new kid and they want to be nice). But nope, once again Serena and Shauna are the ones to get the Starters, Starters they don't even use! Tierno and Trevor probably could have used them, but nah they already got Pokemon so they aren't allowed to have Starters apparently. But seriously, what the heck Sycamore? You couldn't at the very least raise two other Pokemon and sent them with the Starters? And if you're wondering how that would work when you choose first, they could either have the players not realize there was two other Pokeballs until after they picked or Tierno and Trevor could have made a special request so thus they already made their choice. The issue isn't with the Pokemon, its the issue of Sycamore supplying the Pokemon.
 

Celever

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New Mystery: 5 Kids, 3 Starters
So Sycamore asked 5 kids to have them do his field work: Calem, Serena, Shauna, Tierno, & Trevor. Now obviously these kids are going to need Pokemon so Sycamore sends them a set of starters... a set of 3 Pokemon. What? Also why was it decided that it would be your rival and Shauna who would get the other two Starters? Did Tierno and Trevor already have Pokemon? Okay, if they did fair enough, but then comes the time Sycamore gives out the Kanto Starters. Well being Calem, Serena, and Shauna got the Kalos Starters it would only be fair for Tierno and Trevor to get the Kanto Starters (the player also getting one because you're the player, if the needed a reason maybe its because you're the new kid and they want to be nice). But nope, once again Serena and Shauna are the ones to get the Starters, Starters they don't even use! Tierno and Trevor probably could have used them, but nah they already got Pokemon so they aren't allowed to have Starters apparently. But seriously, what the heck Sycamore? You couldn't at the very least raise two other Pokemon and sent them with the Starters? And if you're wondering how that would work when you choose first, they could either have the players not realize there was two other Pokeballs until after they picked or Tierno and Trevor could have made a special request so thus they already made their choice. The issue isn't with the Pokemon, its the issue of Sycamore supplying the Pokemon.
Well, Tierno already had Pokemon and was actually the person who gives the others the starter Pokemon, having travelled to Lumiose to get them off Sycamore and then take them back to the player and their friends, so he definitely wasn't going to take one. Trevor also already had Pokemon and travelled with Tierno to get PokeDexes from Sycamore and bring them back to you, Serena and Shauna. They were already acknowledged trainers when you received your starters, so why would they receive some from Sycamore either time?
 
New Mystery: 5 Kids, 3 Starters
So Sycamore asked 5 kids to have them do his field work: Calem, Serena, Shauna, Tierno, & Trevor. Now obviously these kids are going to need Pokemon so Sycamore sends them a set of starters... a set of 3 Pokemon. What? Also why was it decided that it would be your rival and Shauna who would get the other two Starters? Did Tierno and Trevor already have Pokemon? Okay, if they did fair enough, but then comes the time Sycamore gives out the Kanto Starters. Well being Calem, Serena, and Shauna got the Kalos Starters it would only be fair for Tierno and Trevor to get the Kanto Starters (the player also getting one because you're the player, if the needed a reason maybe its because you're the new kid and they want to be nice). But nope, once again Serena and Shauna are the ones to get the Starters, Starters they don't even use! Tierno and Trevor probably could have used them, but nah they already got Pokemon so they aren't allowed to have Starters apparently. But seriously, what the heck Sycamore? You couldn't at the very least raise two other Pokemon and sent them with the Starters? And if you're wondering how that would work when you choose first, they could either have the players not realize there was two other Pokeballs until after they picked or Tierno and Trevor could have made a special request so thus they already made their choice. The issue isn't with the Pokemon, its the issue of Sycamore supplying the Pokemon.
...It's been awhile since I played to that part in the game, but... I don't remember Shauna or Serena/Calem being offered the other two Kanto starters. If they did, their not using them may be a result of game play mechanics. It's not hard to have Serena/Calem use the Kalos starter with a type advantage against yours, they've only been doing it since Gen 1, but it might have been more trouble than it's worth to have to also account for the Kanto starter you picked. Black/White shoved an elemental monkey on you based on your starter in order to help you against the Striaton City leader's elemental monkey also based on your starter, so it was pretty easy to have the other monkeys already integrated into Bianca and Cheren's teams. Game Freak would have had to program in 9 possible teams for Serena/Calem, and another 9 for Shauna for just one battle. Not to mention neither of them would be able to use the accompanying mega stone until the post game, and even then Shauna still wouldn't be able to.

As for Trevor and Tierno, neither of them are that interested in battling. Trevor wants to fill out the Pokedex while Tierno's too focused on dance moves. Honestly, a few problems with the cast of characters would've been solved if these two weren't in the game. Give a bit of these traits to Shauna and Serena/Calem so they feel more fleshed out, thus have a reason to give a crap about them more. As it is they're the only ones to get any semblance of alone time with you to stand out on their own...
 

Pikachu315111

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Well, Tierno already had Pokemon and was actually the person who gives the others the starter Pokemon, having travelled to Lumiose to get them off Sycamore and then take them back to the player and their friends, so he definitely wasn't going to take one. Trevor also already had Pokemon and travelled with Tierno to get PokeDexes from Sycamore and bring them back to you, Serena and Shauna. They were already acknowledged trainers when you received your starters, so why would they receive some from Sycamore either time?
Ah, I see now. They pretty much skimmed that fact over. Though even if they didn't get a Kalos starter the Kanto starters would have been fair game since by then everyone was a certified trainer. Heck if anything the player was the last one that needed a Kanto Starter as we're apparently a Pokemon trainer prodigy. Heck, after picking the Kanto Starter you should at least have two Pokemon which is more that Tierno who only has Corphish when you battle him (I guess he could have more in the PC, but don't see why he wouldn't have it with him).

...It's been awhile since I played to that part in the game, but... I don't remember Shauna or Serena/Calem being offered the other two Kanto starters. If they did, their not using them may be a result of game play mechanics. It's not hard to have Serena/Calem use the Kalos starter with a type advantage against yours, they've only been doing it since Gen 1, but it might have been more trouble than it's worth to have to also account for the Kanto starter you picked. Black/White shoved an elemental monkey on you based on your starter in order to help you against the Striaton City leader's elemental monkey also based on your starter, so it was pretty easy to have the other monkeys already integrated into Bianca and Cheren's teams. Game Freak would have had to program in 9 possible teams for Serena/Calem, and another 9 for Shauna for just one battle. Not to mention neither of them would be able to use the accompanying mega stone until the post game, and even then Shauna still wouldn't be able to.

As for Trevor and Tierno, neither of them are that interested in battling. Trevor wants to fill out the Pokedex while Tierno's too focused on dance moves. Honestly, a few problems with the cast of characters would've been solved if these two weren't in the game. Give a bit of these traits to Shauna and Serena/Calem so they feel more fleshed out, thus have a reason to give a crap about them more. As it is they're the only ones to get any semblance of alone time with you to stand out on their own...
Sycamore does give Shauna and Calem/Serena the other Kanto Starters:

(After picking your Kanto Starter)
Sycamore: "Come now, you two. Pick your Pokémon."
Shauna: "I don't know which one to pick! It's so difficult!"
As for the rival's Kanto Starters they could have done one of two things:

1. Since Calem/Serena is suppose to be your main rival they'll also get the Kanto Starter strong against your's.
2. Since Calem/Serena got the Kalos Starter strong against yours Shauna will get it this time.

They could have made Tierno and Trevor interesting characters, or at least had them do interesting battles. Tierno Pokemon do use the dancing moves like Swords Dance and Petal Dance so had they focused on that and done more battles with him we could see him as someone who buffs his team (maybe even have him use Baton Pass or his battles could be Double/Triple battles so he could use partner moves). Being Trevor is big on catching Pokemon he could use lots of status ailments, stat reducers, and defense buffs.
 
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Ah, I see now. They pretty much skimmed that fact over. Though even if they didn't get a Kalos starter the Kanto starters would have been fair game since by then everyone was a certified trainer. Heck if anything the player was the last one that needed a Kanto Starter as we're apparently a Pokemon trainer prodigy. Heck, after picking the Kanto Starter you should at least have two Pokemon which is more that Tierno who only has Corphish when you battle him (I guess he could have more in the PC, but don't see why he wouldn't have it with him).



Sycamore does give Shauna and Calem/Serena the other Kanto Starters:



As for the rival's Kanto Starters they could have done one of two things:

1. Since Calem/Serena is suppose to be your main rival they'll also get the Kanto Starter strong against your's.
2. Since Calem/Serena got the Kalos Starter strong against yours Shauna will get it this time.

They could have made Tierno and Trevor interesting characters, or at least had them do interesting battles. Tierno Pokemon do use the dancing moves like Swords Dance and Petal Dance so had they focused on that and done more battles with him we could see him as someone who buffs his team (maybe even have him use Baton Pass or his battles could be Double/Triple battles so he could use partner moves). Being Trevor is big on catching Pokemon he could use lots of status ailments, stat reducers, and defense buffs.
It's still 9 teams they'd have to program in for each, and especially in Shauna's case, only in one battle. If they were to force you to take the Kanto starter strong/weak against your Kalos starter then maybe they could've incorporated them into their teams, but instead you've got the choice between the three, thus 9 teams would have to be programmed in - one for each combination of Kalos and Kanto starter based on the player's choice for each set. (Chespin and Bulbasaur/Charmander/Squirtle, etc.)

If even the Battle Maison AI can't necessarily be trusted with status-category moves, what hope in hell do Trevor and Tierno have? Especially when it's extremely rare that characters below a gym leader (even then often just the move they give you when defeated) get a move set more advanced than the last four level up moves for the Pokemon they're using.

As for Serena/Calem and Shauna not using Kanto starters from an in-universe perspective... maybe they simply didn't want to? The former may have only kept their Kalos starter on hand as it holds sentimental value, but didn't want to have another handout on their team, while Shauna... put hers in the PC and forgot about it. (she doesn't seem all that terribly bright, unfortunately...)
 

Pikachu315111

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It's still 9 teams they'd have to program in for each, and especially in Shauna's case, only in one battle. If they were to force you to take the Kanto starter strong/weak against your Kalos starter then maybe they could've incorporated them into their teams, but instead you've got the choice between the three, thus 9 teams would have to be programmed in - one for each combination of Kalos and Kanto starter based on the player's choice for each set. (Chespin and Bulbasaur/Charmander/Squirtle, etc.)

If even the Battle Maison AI can't necessarily be trusted with status-category moves, what hope in hell do Trevor and Tierno have? Especially when it's extremely rare that characters below a gym leader (even then often just the move they give you when defeated) get a move set more advanced than the last four level up moves for the Pokemon they're using.

As for Serena/Calem and Shauna not using Kanto starters from an in-universe perspective... maybe they simply didn't want to? The former may have only kept their Kalos starter on hand as it holds sentimental value, but didn't want to have another handout on their team, while Shauna... put hers in the PC and forgot about it. (she doesn't seem all that terribly bright, unfortunately...)
Actually a if else/case selection would solve that problem and actually be much more efficient. Instead of making 9 different teams they would just put the Pokemon's ID into the trainer's party array.

Them having a gimmick would at least be more than what they have now. Also don't rivals usually get Pokemon who have "advanced" movesets?

True, Shauna seemed VERY fascinated with her Kalos Starter that she probably prefer spending more time with it. Serena though would put hers in the PC as she's trying to become a Pokemon Master and doesn't want free handouts (too bad the player exists, though at least she mastered Mega Evolution). Still kind of a waste.
 
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New Mystery:

Where exactly do Pokemon go when they enter the PC or a Pokeball? The two must be related, compressing down very large Pokemon and storing them until they are released, but this is only glossed over in the games. We get someone like this,
When they aren't Ratatta mutants.
who lives out in the woods or wherever and works on a large machine. How does it store millions of Pokemon, and most importantly... where do they go? Do they become data in a computer, sent to some sort of kennel, just to the regional Professor's lab as seen in the anime?
 

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