However, there are two issues that drive people crazy:
1) When you go enable full screen mode for an app, the app fills one display and all other displays are blanked with a gray linnen texture. That's may be useful if you are watching a movie and don't want other displays to annoy you, but it's really annoying if you just want eg. Mail full screen on a secondary monitor.
2) Mac OS Lion also added a feature named "Spaces" (I think this is called virtual desktops or so on other platforms). The problem is that when you switch between spaces, both screens switch simultaneously. Now let's assume you use your secondary monitor to show an IM client, or to show some live error log, or similar, it's really annoying if that disappears when you switch between spaces on your main display.
So OS X 10.9 finally makes two features introduced in 10.7 (Full screen mode, spaces) usable for people with multiple monitors.