The desktop window should allow for transparency (or always be transparent and use the root window for wallpaper, as many other window managers do).

This would simultaneously solve many issues people have with programs that draw on the root window, and would enable compiz (or any other window manager) to deal with background, potentially allowing for different backgrounds per workspace or viewport.  These things seem as though they should be logically dealt with by the window manager and not the file management component.

Other information:
I tried to find an existing bug, since I figured someone somewhere must have asked for this before, but the closest I could find was bug 141441.  If this is a duplicate could someone please let me know and I'll subscribe to the original bug.

There were some potential patches available at http://forum.compiz-fusion.org/showthread.php?t=6199, but they don't tie in deeply to the mechanism (for instance, allowing the appearance background tab to set transparent rather than solid colour/gradient).

If there's any further information I can help with, or any patches people would like me to test out, I'd be more than happy to help...  5:)