I'd like to see a game for the Wii that encompasses all prior Regions, so it would have Kanto, Johto, the Sevii Islands, Hoenn, Pokétopia, both Stadiums (the N64 games), Orre, Fiore, the Orange Islands (I don't like the idea of anime-only stuff), and a few new Regions. Hoenn would have the Battle Frontier, like in Pokémon Emerald Version, and Orre would be as it was in Pokémon XD: Gale of Darkness. You'd start anywhere but the new Region(s), go through the Gyms, etc., like the games prior. But then you'd get a ticket to go to the next Region, and keep playing like that.
This game would also have a storyline similar to that of Legend of Zelda games; you play the hero, your significant other (or friend, or sibling, or parent, or whomever) would get into trouble off in the new Region, but you need to go on a journey to prove yourself, raise your Pokémon, etc. until you'd be allowed to go to the new Region where your Zelda (or whatever you name him/her) would be waiting. There would be tons of side quests, tons of tidbits to the story in every Region, and a dangerous new foe who expertly wields a LV100 uber team.
It would also have a Wi-Fi mode similar to Pokémon Battle Revolution, be compatible with Pokémon Ranch (remember Pokémon Box: Ruby & Sapphire? This is similar), be able to communicate with Diamond, Pearl, and Ranger, and you'd be able to train as a Trainer, Ranger, and Coordinator.
The control scheme would be similar to a cross between Pokémon Battle Revolution and The Legend of Zelda: Twilight Princess, and the battles would be 3D. All characters, Pokémon, everything really would be as realistic as it gets (see graphics from Final Fantasy XII).
Finally, Pokémon availability (remember, Pokémon can be version-exclusive) would depend on your choices on personality at the beginning of the game. If you've played Kingdom Hearts, you'd remember the questions asked of you at the start of the game, and it determined what abilities you'd learn at what levels, and how your stats would grow, and how fast you'd level up. Well, similar case here. Your choices reflect what Pokémon won't be available, so you will need to do quite a bit of trading.
THAT is what I'd like to see. And yes, geckoriot has a very good point about deeper plots and such.