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Story-Related
- If the Dark Synergy Stone absorbs all the Synergy in Ferrum and is capable of fusing itself with living organisms to make them uncontrollably battle-hungry, why haven't Anne's tribe tried destroying it? I would say it's because of a Yin-Yang thing and that it's needed to prevent too much Synergy from flooding Ferrum, but all implications suggest that the balance is already kept in check by the constant Ferrum Battles that take place.
- Suicune. Sure, it is normal to allow Mirror Matches in a Fighting Game, but it is still weird to see two Suicunes fight each other, without anyone lampshading it, not even the fact that even one trainer (like the Boss trainer Keith, who by the way manages to not be the best trainer with it and wastes its potential) captured a legendary and unique creature.
- The same could be applied to (Shadow) Mewtwo, but there is actually only one canonical iteration of the character in the game (while the presence of two Mewtwos could have been justified by the "female" one from the anime).
- However, the dialogue in the game still uses the term "A Mewtwo", and other terms implying that Mewtwo is an accepted species of pokemon, as opposed to a single unique Pokemon.
Gameplay
- The playable Pokémon use Red/Green/Blue (the theme colors of the game) as variations on their traditional colors for their Player 2 colors, even though it would make more sense to simply use the Shiny colors of the various Mons instead. True, it wouldn't work for Pokémon such as Pikachu whose Shiny form is so similar to it's regular colors, but still.
- Considering they *gain* the color right before the battle, it seems to be a League-Regulation, where mirror matches are given a temporary color change via tech to distinguish the two
