Odds are no one will agree with me on this, but I would take Michael Vick. While he's not the best passing QB, he can take off and run for first downs and the defense has to respect that. He also rarely ever gets sacked which is a killer for the 2 minute drill. Vick is also fast and quick enough to slip out of bounds if he needs to. I think that the defense has to respect Vick's running ability enough that it will open up some gaps in the secondary.
That being said, I would also take Peyton Manning or Tom Brady without a second thought too.