A new update has fixed a major bug in Ubuntu 12.04 that was causing reduced framerates in 3D games and applications in Ubuntu 12.04.
This was a performance regression specific to the Unity shell plugin. While enabled, graphics were slightly choppy and did not perform as well as Gnome Shell, Fallback mode, Unity 2D etc. A drop of about 30-40% had been noticed in framerates of some 3D games. This bug was mainly affecting NVIDIA users but some users have reported similar performance issues on ATI cards as well (though I am not experiencing any performance issues with fglrx).
A fix for this bug has been released in the latest Unity update in Ubuntu 12.04. Do note that the fix will not magically improve your max 3D performance which is limited by your hardware/drivers but it will take care of any drop in framerates introduced by the bug.