I thought I was going to return my rMBP until I actually miraculously fixed mine!
• So I was suffering from the usual choppy laggy scrolling, when I decided to connect my rMBP to a Thunderbolt Display (I was lucky to have access to one at work).
• I closed the clamshell lid, restarted the machine and entered into the Restore partition from the Display.
• I ran Disk Utility and ran disk repair 3 times, on the second repair it revealed that it had serious error.
• I fixed those repairs on the run and ran it a fourth time to make sure there were no more errors (keep in mind this is off the Thunderbolt Display)
• Then I ran the permissions repairs 3 times, until no errors appeared.
• I exited out of Disk Utility and proceeded on Reinstalling OS X.
• After restoring the laptop I disconnected it from the Thunderbolt display, ran the Supplemental Update 2.0, the lagginess returned, but I repeated the entire process from above and restored OS X a second time, and ran the Supplemental Update while connected to the Thunderbolt Display. After disconnecting the display, SUCCESS! I swear to the gates of heaven above my laptop is healed!!
I have been running it for the past 6 hours running test after test after test, from Photoshop, to iPhoto, to browser scrolling, there is absolutely no lag! Unigen Heaven 3D test is at a staggering 48 frames per second (I got 8 or 9 before) and Photoshop has that legendary inertia scroll that we all love. Most importantly, when every time I restart my laptop, the screen no longer blacks out before it smoothly scrolls its way onto the Desktop! I'm like WOOOOOO!!!!
If you have access to a Thunderbolt Display, give this procedure a try, and let me know if it has helped you or not.