I personally want to see a game that takes you through each of the regions, and adds new regions. That each region adds to the list of pokemon. I don't mean to say we add NEW POKEMON to the list, just to say that in Kanto you start with the 150, and as you progress in the game, your pokedex updates with the region with the next generation of pokemon and so on.
It'd be nice to be able to create your own character, as well. I've got a full sprite sheet of my character, Okami, that would be so fun to actually find a way to use in-game.
To see the crossing of all of the regions would be nice, because it would add longer gameplay (As if any of us need that, I've got 400+ hours logged into Diamond alone, and 40 logged into Platinum as of right now) And perhaps we could see the relationships of the professors in clearer detail, and show how all of the pokemon myths collide.