I've been playing thru my BW2 recently, and I have new demands for small details in X/Y.
1) During sea battles, when you send out your Pokémon, it should make a splashing sound. I'm tired of sending out my Lapras in water and it sounding like I threw it onto a steel grate!
2) I don't think the 4-move per Pokémon mechanic should be abolished, but I do think that you should be allowed to teach your Pokémon 2-3 extra moves, in reserve, that you can substitute at will for your 4 moves.
3) Whatever HMs exist in Gen 6, we should be able to make our Pokémon forget them without the need for a move deleter. At the very least, GF should grant the player the ability to forget HMs around the 3rd or 4th badge.
4) In the post E4 game, I'm tired of the trainers you meet having 1st or 2nd stage Pokémon, regardless of whether the Pokémon are from foreign regions or not. I understand that the game is allowing you to complete your National Dex by doing this, but I find some of the battles become stupid and repetitive. I'm tired of battling Lvl 65 Cubones, Slakoths, Lotads, etc. Its the end-game for crying out loud, the vast majority of trainers should have well-developed, diverse teams. In order to help you complete your Nat Dex, they should just make more foreign Pokémon available in the wild post-E4, or create more Nature Preserve type areas.
5) Drohn made a comment above about modifying the use of Fly outside of battle. I couldn't agree more. Plus, who wouldn't want to do that?
6) Even though it doesn't seem likely, based on the available info, I want the main rival character to be a total jerkwad. To this day, I'll still argue that Blue and Silver were the best two rivals in the games, and its because I took so much pleasure in wiping the floor with them. In the context of X/Y, I'm hoping that, after starting their journey with you and your pack of friends, your rival somehow stabs you in the back and joins Team Flare or becomes a Flare sympathizer.