Perhaps you could use the two analog sticks to control the two characters and use the two triggers for jump (so you would essentially have the left side stick and left trigger for one character and the right side stick and right trigger for the other). That might be just funky enough to be fun...
Sounds like a good configuration, but controlling both at the same time is pretty difficult stuff I must say. But you could start of easy and slowly train the player into multiprocessing.
I think it's safe to say there would be a significant learning curve to have to control both, though most FPS games on the consoles require both analog sticks and several triggers, face buttons, and sometimes even bumpers, so I have faith that people are not all completely inept (just me). Good luck with the XBLA thing if you go that route!
Cheers,
--Zack