I would definitely like to see the game span all five regions and the 'auxiliary' regions as well. This would take easily a hundred hours and would allow for some gyms to be level 90 or so. Someone else also had this idea, but you could pick where you start and thus would get to choose particular pokemon based on that area. Maybe different starter types for the new one, but the same fire grass water for the others. It's certainly easier to remember but for older players it get really boring.
I'd certainly like to see more abilities, more strategies in game, and more ways to overcome 'cheapo' type stuff. More legendaries would also be good, but interesting that really had a big impact on the game rather than just a token. Also, I liked the idea of not having to get everything at a nintendo event, but it should definitely be quite difficult.
Lots of sidequests also. Oh, and they have to drop the really corny names like 'Bronzor', 'Baltoy', 'Nosepass', 'Bidoof' 'Budew', 'Burmy', and such. Get more innovative. Maybe one or two extra basic critters but I think we're up to here with them (just making more from more generations appear would be more than enough I think). Moves need to stop ripping off of each other; instead of just making a water/fire/grass/dragon hyper beam maybe they could have completely new moves. Also, if your leading pokemon's level is really high you could just have an option to auto run from all low level pokemon you encounter (so you can just walk through grass). It doesn't make much sense for level 5 ratattas to be attacking your level 80 metagross.
Being able to carry everything is REALLY annoying, the item storage needs to be brought back. Also, having a million pokemon that need to be traded to evolve gets annoying too. More ways to evolve should be invented; I liked the mount coronet and moss/ice rock things. It also needs to be shown HOW to do this so not everyone has to look up walkthroughs for it.
I could see perhaps one or two new types being introduced, but it's not a big deal and this would probably be difficult. One could possibly be 'gas' or something, but I really don't know how well that would work (it's too much like ghost and poison). Some new evolutions (Rotom, Parasect, Carnivine, Claydol, Drifblim, Quagsire, Octillery, Kabutops, Omastar, Kangaskhan, Absol, Skarmory, Lunatone, Solrock to name just a bunch) or evolution trees would also be nice. I'd also like to see the new 'heavy dragon' type of this game be very different than the past ones with a new type perhaps. Some new type combinations would also be good, but this isn't really a big deal.
The 'evil teams' also need to be much less corny and much more sinister.