Mission Control needs to change.
I concur with the people who have pointed out the uselessness of external displays with fullscreen apps (that aren't designed for multiple displays).
Come on, Apple. The Mission Control UI is broken. Fix it.
We should be able to switch desktops for each monitor separately. Heck, it would be nice to move desktops from display to display, if the displays had the same resolution (or even if they didn't, perhaps by telling fullscreen apps to leave and re-enter fullscreen mode).
I'd like to keep a development VM on one screen, while switching between references on another... but as it stands now, I can't.
EDIT: To be fair, the same was true in Spaces, though I could have a full-screen app on one monitor and still use the other.