Hi all! Just wanted to share my story regarding the same problem.
Got my MBPR 15' refurb a couple months ago, packed with 16 gigs ram, 2.6 ghz processor, and a 1 gb 650M videocard. After a couple weeks i noticed that UI lag, which was just unacceptable for how much money i've bought it for. So I went to the Apple Store in downtown Toronto, a genius bar guy examined it, admitted the lag, and grabbed it for hardware test. As i came again a couple days after, he said the hardware is fine, but he cleaned the coolers and tightened up the screws holding the screen. So i went home and saw pretty much the same thing.
After a Christmas vacation, having reinstalled OS X, i came in again, and said bye-bye to my mac for another week. This time, they've replaced the logic board, which showed no result either. Then, having taken my laptop again for another week, they've replaced the screen, which, guess what, had no result as well. After that, i was visiting the Store so often that pretty much everyone there recognized my face. Every time the technicians were saying that according to tests, EVERYTHING worked fine, and they just refused to see ANY lags, whereas at the beginning they were admitting overall choppiness of the system.
Last time i've been there two days ago, and i completely рissеd off one of the genius bar fellows, and so he finally called out a manager for me. I had a nice long conversation with him, and he finally agreed to replace my MBPr.
This is how my first Mac experience went. It's pretty disappointing to save for a couple months, then pay $2200 for a laptop and work on your old 2009 Asus instead, while your brand new notebook just sits in service all the time. And i'm just not saying how much time i've spent coming to the Apple Store every week.. If this new Macbook does not perform well either, i'm going to sell it and forget about Apple laptops forever. Such a waste of money..
So im waiting for my new computer to arrive, and i'll keep you guys posted when i get it, and tell if i have bad GUI performance on that new machine as well.