Same issues here, got my new rMBP 13" yesterday and noticed some extremley annoying lags using the basic Mac OS tools. I don't understand why this problem is not a popular issue, if every rMBP has this problems.
Before buying i was curious about the performance of this machine, but the performance is great. I played some simple games and used the Adobe CS6 Suite and it works all over great. I know its only the HD 4000 but it's totally OK, but the UI lags make this machine not useable at all.
My roomate owns an 13" MBA and it works totally smooth compared with my rMBP. I have no idea why apple is selling just idiotic machines like this.
By the way: I love the retina display and I love the design and quality. But I don't understand why I should spend over 1,5k to have lags in the everday use.
I contacted the support 2x. First I had to reset the PRAM. Doesn't work. After that he offered me to send me a new one, of course: without lags. I told him that I have really no interest in waiting 2 weeks for another sloppy machine. So he told me to ask someone if there is any software update in developing that could fix this issue. After he placed me on hold I lost the connection...
Second genius told me to start in secure mode, the lagging got even harder. His expert opinion is that my rMBP has an hardwaredefect, and I should get a new one, guaranteed without lags. I told him the same, but he answerd that the rMBP's are totally great computers and normally they don't lag. After that discussion he told me to reinstall Mac OS and get a new one, but nothing changed.
I tried different fixes as well. Installing AutoCAD, doesn't work for me. And deleting some files and deleting PRAM after that doesn't work for me, too.
Tomorrow I will send my rMBP back to apple. And probaly I will order the MBA 13" and save about 400€. Sad story, I really liked the retina