I don't think you should have direct control over your pokemon, but command then in real time (speed would be a more meaningful stat!). Sure you would be able to give a few more commands than in usual games, but still not be overly-specific. In a perfect world the pokemon would have a learning AI so that they'd get more than just metaphysical experience out of battles, and actually carry orders in a more effective way or know what to do when you don't give an order in time either because you can't decide, is getting an item, or it's a 2 on 2 fight or maybe a 'no orders given gym fight' or something. Also, cut the number of pokemon a bit and balance it well :P
Anyway, I'd like a real-time game on console, and there would still be room for TB ones on handheld.