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fix the damn idle animations and models of a bunch of pokemon, mostly "flying" pokemon.
on the game itself, i'd bring back hard mode, available from the start, and make the teams for trainers actually decent, not just mons with their latest 4 learned moves. not extra challenging just for the sake of it, but not a walk in the park either, bring back gym leaders rematches, vs seeker, PWT, make an in game battle simulator (basically showdown, so you can try out things without biking, maybe even add an online option to it), give megas to all relevant trainers at some point, and add more new megas since they're here to stay.
And some balancing stuff that may fit better on a new gen:
Buff shitmons (not just in the form of megas), stop the power creep (nerf parental bond and the type-ate abilities damage multipliers a little and such), give hail a secondary effect like sand, change some odds of secondary effects and confusion, add 6v6 to battlespot and battle facilities, maybe create a few new moves/abilities, and make terrains not so fucking useless