For instance, application windows cannot be used across multiple monitors anymore -- windows can only be used on one monitor at a time.
I think this thread is illustrating why multiple monitor support & full screen worked the way it did in 10.8: any other solution is a can of worms requiring lots of options to suit everybody.
You can see how these problems arise if you think about it (and that's without knowing the technicalities of how this stuff is actually implemented):
In ML when you 'full screen' an app, it creates its own 'space' (spanning both screens) - which is great, because you can use spaces to flick between full-screen apps (including any of their palettes that you've dragged onto the 'spare' screen). So if you allow a different full-screen app on each monitor, you pretty much
have to give each monitor its own set of spaces.
If each monitor has its own set of spaces, and windows can overlap monitors, things are going to get
really hairy.
Now, take 3 monitors, full-screen an app in the middle monitor, then extend a window off the edge of the left-hand monitor. Where does it go? Now de-full-screen the app in the middle. What happens then?
Erk! better just stop windows spanning screens.
UI design is
hard.
Personally, although I was originally miffed at the way full screen turned off my second screen, it then started to make sense. Firstly, it was mainly useful for people with small, single screens (Airs etc.) who wanted to concentrate on a single app, maximising screen estate and reducing the use of floating windows. If you've got multiple 24" monitors, just use the little green "+" sign that we've had since forever.
Or, if you have multiple screens and do want to use a full-screen app, use your second screen to park all the control palettes, and fill the main screen with your work. Then use Spaces to flip between programs. Works great with something like Pixelmator (wonder how that works in the new regime?)
Good job they left an off switch.