I hope this helps someone...
I rarely post here, but after weeks of experiencing the performance hit post EFI update on my rMBP I wanted to share how it was resolved. Hopefully it helps someone here...
Issue:
Since day 1 (back in Nov) my MBP was able to run pretty much any game, stutter free. Post EFI update, the games would start to stutter in bootcamp, but not in OSX. In Windows 7, I saw that the GPU temps would reach 95-98C and the clock speed would throttle down from 900 to 250ish over and over, in perfect sync with the stuttering. While in OSX, reaching those temps caused no throttling. Before the EFI update, I remember my GPU always reaching mid 90sC while playing games, but there was no throttling. So I figured the EFI update was the cause, and only in Windows. Well, yes and no...
Nothing I tried to do to fix it worked. Full re-installs of both Windows/OSX, beta drivers, legacy bootcamp drivers, underclocking the GPU (this sorta worked, temporarily, but games were still unplayable) and cleaning out dust. Nothing worked, temps still were in the mid to high 90s and the GPU would throttle.
Solution:
On my second trip to the Apple Store, I explained everything and showed the Genius the stuttering in any game in Bootcamp. While the diagnostic tools showed no flaws, he also owned this machine and knew that my performance was not the same as his machine's, so he took it in to replace what we thought was the culprit, the heatsink and re-apply thermal paste.
5 days later, I picked up my machine, fired up a game, and the issue was fixed. Not only fixed, but I was now able to max out settings in games I wasn't previously able to max out! I ran nvidiaInspector and was shocked to see that my GPU now NEVER went above 80C, even while running games at native retina res with high settings!
In the end, I believe my rMBP always had a defective heatsink and poorly applied thermal paste, causing the GPU to reach 95-98C, but with no throttling. Post EFI Update, I was now well above the new throttle temp, causing huge performance hits. Replacing these parts and seeing the difference convinced me this was the cause.
I'm now pleasantly surprised that I can run games like Skyrim, Tomb Raider, Sleeping Dogs, Dishonored, etc... on high and sometimes "ultra" settings and my GPU never goes above 80C. I believe this is the way the rMBP is supposed to work. Anything higher is a defect, which shows symptoms post EFI update.
TL;dr - Going to the Genius Bar to have them replace the heatsink and re-apply thermal paste fixed this issue for me. The rMBP should never go above 80C, even when playing games on high in Windows.