I like the turn-based way, but real time would be awsome. I can only see one flaw in it: increased double KOs. If Pokemon attack at the same with moves powerful enough to KO each other, there's no winner and no EXP. Turn-based gives you one solid winner every time (excluding Selfdestruct, Explsion, etc. that are MEANT for both Pokemon to KO.)
Real-time gives cool counter options, though. This is both good and bad. If there's nothing but counters in a battle, it could last until both Pokemon have no moves left. Since this is a game, however, the Pokemon won't get tired and can even counter each other's Struggles. On the bright side, it would give the games a more realistic effect.
I'd say yes to real-time on games like XD and the Stadium games, but no on handheld games. It would be harder to do on those, and with how the Pokemon are placed you can barely see the counter anyway. Do that with a 3D game, and oyu've got something great.
Wow...I sound smart...