I think Game Freak and Nintendo have done an amazing job with gen V, specially with the pokemon balance, even if some of them are really ugly at least statswise it's really not like in other versions where they had filler pokemon (ehem....Farfetch'd, Luvsic, Chatot...etc ). Where I feel the game is still laking is in terms of customization. I mean, I've played YGO: WCG 2011 where you can modify your NPC, I'm not even asking for thousands of options, hell that game has about 10 for only 5 items. I'm asking for something like in PBR, change some things so we don't stand around in clones.
The other thing I would like to change, since they have eliminated capsuńes is the pokeball a pokemon is caught in. Yeah sure, I used a Great Ball to catch it, but maybe the effect of another ball looks cooler, so let me discard the one used to replace it with the new one. Personally I would have Dusk Balls all around, how cool would that be?
I think these would be a great addition for Gen VI, since there isn't much where they could go from Gen V, battlewise they introduced Wonder Launcher, Triple Battles and Rotation battles, which give you an idea of how the battle system is almost where they want it to be. I really don't see what else they could be adding to the game besides that to give Gen VI an appealing factor.