Hm...I guess a new clothing system would be nice. Seeing the different combination of clothing you put on your character before entering a battle would be intersting. Of course, it would be for aestheic, it doesn't affect how the Pokemon battle.
I like to see Pokemon like Qwilfish or Corsola evolve. LOL And finally giving Miltank and Taruos their SHARED pre-evolution stage.
Also, a dark type gym leader. I still can't believe; seeing how long Pokemon been out, there STILL isn't on yet...I mean, damn!