1- A new default HUD, more clean and modern, for overworld and a visual update for the battle screen, i recommend the Concept HUD from @Starnacle, he has a cool post about it, his concept encompasses both areas
2- Battle Replay system: A system to save your battle replays and send them to your friends or team, that would be really usefull for the game
3-Some habilities like Cradilly's Storm Drain and others that aren't unbalanced, that could give a new life to some pokemon like slowbro, cradilly, tangrowth regen, etc