I just saw the Reggie interview from G4 yesterday (I know, I'm slow). His clue about the controller was to think about a controller that could play all past generations of games.
First, it implies that the virtual console aspect isn't just a cool thing Revolution can do. It sounds like an important strategic move if they're going to base part of the controller design around it.
What about a modular design? Keep the left side's D-pad and control stick... but the right side detaches, and you can swap it with other button configurations or features?
It sounds a bit too Frankenstein, but it was the first thing I thought of. Just yacking out loud.