One problem I’ve found while using Unity with patched Nemo is that upon changing the desktop background, compiz seems to hard-freeze. Not even restarting lightdm can one get out of it, either go down to to ttyx and kill -s9 compiz, or reboot.
I believe this might be related to changing the background for the user at lightdm, as it reverts back to the default image (I do have the gsetting btw), whereas if I switch back to Nautilus it works OK.