- Further implementation of 3D. Remove the grid and give a controllable camera. This game is 3d, but there is essentially nothing in it that couldn't have been easily accomplished in 2d except for possibly the gyms, which really are not that exciting.
- Removal of random battles. I know they're a staple of the series, but I've been wanting a full fledged Pokemon game where you can find Pokemon on the map ever since Red and Blue. I feel like it would be a lot of fun to actually find Pokemon living in their natural habitats, possibly using different items and things to lure them out and engage them.
- Dramatically increased difficulty, probably in the form a hard mode option like others have said.
- More maturity in the dialogue. No, I don't want the characters to be cursing or anything like that, and the game should definitely keep its E rating. I mean maturity in the sense that the conversations should be deeper than just like "You need to stand by your Pokemon friends!" The dialogue needs to be more nuanced, and there needs to just be more of it in general. Sure, quality is more important than quantity, but you just can't get that much depth when conversations max out at like 3 simple sentences. The core plot to this game is honestly as deep as a lot of bigger RPG plots-- it's just the simplicity of the presentation that is holding it back.
- Some sort of change in the plot. I think the core gameplay is fine, but it doesn't always have to be 8 gyms + Elite Four + Team <whatever>. Just do something, anything, differently.
- Several GTS improvements are needed, including blocking players from requesting impossible things and giving the ability to "reverse search," or find all the Pokemon that you could get for one of yours.
- Remove IVs entirely, and make EVs, natures, and so on even easier to track and understand. There needs to be an in-game explanation of these features-- it makes no sense that you have to look to outside sources to understand them. Post battle, you should be able to see what EVs you gained, which can simply be done in the form of a more detailed post-battle screen like you'd see in any typical RPG like FF or Tales.
Whew, that is a lot of stuff. I really like this game and the Pokemon series, but I feel like it could be so much more. The core gameplay is great, but a lot of the surrounding functionality is starting to get really dated and repetitive, in my opinion.
I'll probably always be patiently waiting for my dark, gritty pokemon game. Make the actual brutal pokemon war the vehicle for the game's story, and not just some event that happened in the distant past.
Significantly harder difficulty.
Essentially, a game for some of the older fans that only still play the games because the gameplay is enjoyable, and not so much for any sort of challenge, interesting characters, depth, or decent storytelling (not to say that a story needs to be dark and gritty to be good, but that's what I personally prefer).