Pretty nice idea. After all, the basic system is very similar. You just spawn and despawn mercs with throwing pokeballs- not a big deal. The only problem I'd see is how to control the critters in combat. Maybe the player should get direct control over them and use them like a player character is used right now. I could think about quite a few workarounds to get that done, but it's some fiddle work.
With 3d model support, it isn't even such a big deal to create new charcters and creatures.
I'd say such a game is definitive easier (and more interesting) to make than a "FOnline: Whole world can be traveled" game. :>
