Just stick your model in the simulation when using a cloth simulator. Then you animate the cloth while the model is going through it's animation.

Bring the whole object into MED as a vertex animation and it should look right. Keeping the cloth out of the model isn't difficult in XSI. That's the only cloth simulator I have access to. (besides the one the comes with truespace. But I'm not going to load that one up right now.) On second thought I also have poser 5 with cloth simulation. It's an ok animation system, but not as good as the XSI cloth animation system.

I agree that a realtime cloth animation system would be really cool to use in a game. But this is the best that I can think of for the time being.