Not to completely dismiss this but … have you noticed how much extra burden this places on developers and how this is almost always cited as one of the reasons why the OSS desktop experience isn't as good as OS X? There are many parts of the desktop experience which require more than cursory integration and that becomes a much harder problem to make generic and plugable.

Do you mind mentioning some examples. My desktop runs Awesome, but I make extensive use of Gnome widgets and programs. The fact that these work out of the box without issue, despite the fact that they were developed to be part of the Gnome desktop, seems to suggest that the standards work fine.

Besides, thinking back to when I used Windows, I cannot think of an application/desktop integration that does not work on Linux.

I always imagined that OS X had a "better" experience because it had teams of developers whose job it was to make it have a better experience for the user. Also, never liked the OS X experience, icons don't automatically un-clutter in folders, it is difficult to tell the difference between what is and isn't running, and I still cannot figure out how to reliably rename a file without using the terminal.