My idea for a Poke'mon MMO, would be just like the gameplay of WoW, but with Poke'mon theme.
You start out with no Poke'mon, and you have to go out and actually catch one. The Poke'mon are just out in the open, like animals in WoW. You can have 6 Poke'mon on you at a time, and when you battle with one, you use it's powers, like spells and attacks, down on your action bar.
Perhaps have Poke'mon levels, and Trainer levels. You could only catch a certain level range of Poke'mon if you had the right Gym badge. Maybe your Gym badges would actually BE your Trainer level. And then once your Poke'mon reach certain levels, they could do certain things. Like Fly, Surf, even Ride. A mountable Poke'mon could learn Ride at a certain level, and thus act as a mount.
Battles would be out in the open, not like a private scene, like in the games. Out in the open, just as if you aggroed an enemy. You'd hit a hot key to throw a Poke'ball containing the Poke'mon you desired, and an action bar would appear accordingly, and you would hit moves with cooldowns and such.
Maybe not exactly like WoW, but similar. I really liked Vanilla WoW. And if I could just replace every aspect of that game, with Poke'mon themes and abilities, I think that would be the perfect Poke'mon MMO