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).