I sometimes use two different Desktop Environments like Unity and Gnome Shell (comparing, testing, creating screenshots, etc.) but Unity looks bad using Adwaita theme, which is the same with Gnome Shell and Ambiance theme. Changing every time is quite a hassle and sometimes (but now less frequent than before) it crashes (I'm using Oneiric).
Ubuntu – Is it possible to have different GTK+ theme in Unity and Gnome Shell
gnomethemesunity
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Best Answer
You can try creating a script which you set to execute at each starts where you recognize which DE you are using and switch the theme in base of what you are running