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Size-accurate models.
Being able to turn off Amie/Refresh buffs.
Evolution mid-battle.
More robust option settings in general.
Actions taken by the player effect the world.
Better storytelling (By using the environment, visuals, teams, items, etc instead of everything being obviously written out)
Better gameplay and story interaction (more of the characters talking and walking alongside you like that one stretch in XY, less of the long, annoying dialogue with nothing but people standing around like the rest of XY.)
Actually breaking the mold with the games instead of just slightly editing a feature that basically disappoints half the fans by it being too similar and enrages the other half by being too similar while still removing something (Like totem battles vs gyms, and now there are no gym leaders nor any badges in Alola.)
Actual continuity (instead of vague recurring characters (like Looker and Cynthia) that end up doing nothing every gen just so they can show up the next gen to progress the "story") by making the world reference events in other regions and mention progress on certain things or the whereabouts of specific trainers - as an example.
Actually focus on the usable Pokémon and battles. Introduce a lot of variety for players coming in to use new mons and new gimmicks while not breaking the game by making it too easy or straightforward. XY and USM did this the absolute worst way possible - introducing very few new mons and making the gimmicks very strong to the point that battles are trivial, making the games not engaging in the slightest.
Learn from other games - PLEASE stop living in a bubble because "haha we are small company XD prease buy our game XD" and go out and do research. Look into what people actually want instead of playing on your iPhone for 20 minutes and saying "oh so dis is what peopre want? XD"
God, Gamefreak, Creatures, and TPCi make me mad sometimes.