In the past I have had three important applications having problems with compiz and the proprietary Nvidia graphics driver, they are; Googleearth, The Secondlife client and Blender, compiz and the old shell have come a long way and the performance of these applications when Compiz compositing is turned on is now largely acceptable.
Given that you have decided to use Compiz with Unity instead of Mutter, Will you be testing these or any other important 3d applications with Unity using Compiz and Unity Using Mutter to see which gives the best performance? Tests like these could help to make your case. so far I have only heard of the better hardware compatibility of Compiz and suspect that it will be a better compositing system for Unity.
How the above two configurations compare with the latest Compiz on the old shell and A test of Gnome Shell using its Mutter compositing running these applications would also be useful for comparison. Maybe someone at Phoronix could help in this regard if scientific presentation is desired but a honest personal experience being reported from such tests would be immensely useful I think.
I know it is early days and I do not know the status of Unity with Compiz I surely hope we will not have to go back to the old days when it was a must to turn off compositing to get work done when using certain applications,especially since the Unity shell will be more dependent on compositing than the old shell, in other words what if we have to turn off compositing to use say, Blender,what will happen?
Here is hoping that we will not have to wait another long time to get Unity/Compiz working well with applications that need 3d rendering.
I don't know how it may impact some specific apps, but in my case (I have a ATI 4850), running Compiz instead of Metacity was MUCH MUCH faster. This is because the window drawing job was done by GPU instead of CPU. However, since GPU is doing something else than rendering stuff in google earth, it's performance may decrease a tiny bit. Thats why in Windows when you open a game, it disables transparencies and fancy stuff.
With a properly performing video card driver there should be almost no decrease in performance for regular applications. Video games running at 100 frames per second are certainly going to see a performance loss due to the extra copy and communication involved but there is no compiz-level solution for this.
In reality, Mutter and Compiz use a similar compositing engine, so you are going to get the same kind of slowdowns on each window managers.
The only real solution to the slowdown problem is a hack which places fullscreen windows on top of our openGL scene. However this means that you can't draw notifications or anything up there since they need to be painted in the openGL scene.
We should look into exposing GEM buffer objects as FBOs directly to compiz rather than exposing them as pixmaps. This will get us the few FPS boost that we need to display those applications at full speed. This will be far in the future though.