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Honestly I think a lot of my biggest problems are actually superficial ones.
The Pokemon models of course have been talked about before. Changing colors and animations is great, but I would also like for them to fix the scale of the damn things. It's really dumb to see something like Wailord be that small. It's a turn-based game, a huge model isn't obstructive to gameplay. The camera zooms in and out anyway, so you might as well make use of that.
I'd also really would love to see them get rid of that stupid circle underneath Pokemon during battle and place them in "actual" fields. Is there any good reason other than tradition to keeping those? They're a real eyesore. I dunno, it just bothers the hell out of me that they keep that even though it's not necessary, nor does it tickle my nostalgia bone.
Now that they're using 3D graphics, stop using the dumb overhead view, it completely defeats the point. A behind-the-head camera, or better yet one you can control would allow players to appreciate the environments a lot more. If using a fixed camera, make sure to design the maps so you can avoid an issue that exists with some of the Azure Bay- sometimes its really hard to tell where the you are.
Finally, probably most important- have a strong "theme" which the region is built around. I think my biggest problem with Kalos is that the "theme" of the region wasn't as memorable to me as Hoenn or Sinnoh. The former with the sea/land theme and the latter with the snowy areas and lots of caves. Unova's "completely new region with only new Pokemon" idea was great too, I wouldn't mind doing that again.
