I'm repeating but feel the need to voice,
My practical suggestion would be : Dont make an App Bundle if there is only one app in a space, just do regular expose - that would fix it.
This case of 'single app, multiple windows in a desktop' is clearly broken now because: when you hit mission-control, it actually uses LESS screenspace to show you useful content!
another 'fix' would be to make the bundle-expansion automatic as the cursor glides around much like the zooming dock.
Up until my Lion install (i put it off and now I know why..), I was finding my 13" macbook pro's tiny 1280x800 screen punched well above it's weight, thanks to expose+spaces ability to effecitvely give you 2 zoom levels allowing very natural, intuitive grouping & efficient searching.
Throwing the cursor into a hot corner,zooming out and using the 3 finger drag on the trackpad to shift windows around was as good as it gets, better than any permutation I can find in windows or linux. Better than hiding/iconifying or using z-order control, or using sticky windows, or pulling them across with edge-warp. better than Ubuntu Unity or Gnome-Shell.
I can see that Mission Control is optimized for using fullscreen apps+root desktop ( perhaps inspired by the Commodore Amiga interface from 1985 🙂 .. complete with the partial scroll .. ) with traditional desktop windowing evidently considered as a 'legacy fallback' but even with improvements to xcode (like the tiled assistant editors), xcode is still easier to use with multiple windows open; it's the best way to 'bookmark' IMO, and easier to just use the windowmanager feature than have to find another hotkey within a program.
A good windowmanager is universally applicable once learned.
(I imagine this benefit would have applied to image users even more.)
I dont find it convinient to have many fullscreen windows of a given program because their thumbnails just get unusably small.
'show all of application' doesn't fix it because you may have many of a single app, and you wanted to group them e.g. many sourcefiles within code modules and 1 module per desk.
The 'bundle expansion' is a pain because it's 2 gestures.
(the way it handles multiple monitors is the one improvement)
If they were trying to simplify/streamline with missioncontrol, it doesn't - they still felt the need to keep 'show all application windows' (i really hope they dont remove that!)- and they have additional mechanisms for selecting windows of an app -launchpad, dock, app-bundles - I say some of this is extraneous.
Now when doing iOS dev I'm missing the way Linux works, where every component of the OS can be chosen and replaced by the user from a multitude of options (...and if you have a better idea you can just fork someone elses' code & write it)
I have another idea for desktops inspired by spaces, (0 chance of seeing it in mac/windows but maybe i'll try it in linux..) - to show spaces like mipmaps when the number goes above 2x2 .. so you have the most recent 3 shown as quaters of the full-screen, the next 3 as quaters of the lower right corner, etc. You could slot N fullscreen apps into that easily. I suspect that's far too quirky to ever appear in an apple OS though.