I was also having the exact same issue. I have the 2012 15" Mac Book Pro with Retina display.
I tried the disabling 3D Graphics. The only issue I had was my ubuntu which was running in vmware was incredibly slow (I assigned the machine with 4gb memory).
So i reinstalled Mountain Lion OSX, one good thing about Apple was it didn't wipe any of my content. The installation took 20 mins from the apple store. This essentially rolled back my 2.0 mac upgrade. Now Ubuntu is running fine with 3d graphics enabled.
In case anyone else is interested in rolling back Mac 2.0 update.