With Doom 3 we see right away that there's a small but noticeable (6%) OpenGL frame-rate difference between using Unity with Compiz and straight-up Unity 2D.
Nexuiz was also faster with using Unity 2D instead of Unity, but now Unity 2D is being killed off.
With the old OpenArena 0.8.5 game, there's no performance difference between the two Ubuntu desktops.
The newer OpenArena release is surprisingly faster with the default Unity.
The results were close for Prey, but neither desktop led to a playable frame-rate for this Intel Core i7 3517UE system with the current Linux graphics drivers.