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I would like extra side quests, like "Show me a Flabebe holding a purple flower" or "Please bring me a potion for my pokemon!" and they would reward you with like stones or special healing items, like a pokepie or something you can use in Pokemon-Amie.
Also, I would really like to have a pokemon have a chance to drop their items if they faint, chances could raise if you have a pokemon with a certain ability out.
Additionally if I'm surfing on a Blastoise I was to be surfing on a Blastoise! As well as flying on a Pidgeot! Not some dark blob representation of a fish or bird.