Extensibility, platform agnosticism, avoidance of integration into the OS, etc.

Hmm. I for one think GUI integration into the OS is what could actually make Linux a viable option on the desktop. Apple and Microsoft GUI's are integrated into the OS, and they work. They're simple, they do what users want.

X is a big fat pig, and it, along with the many incompatible GUI layers on top of it (some of which you've mentioned) are the main reason why *NIX will never be able to make inroads on the desktop.