Today I have been in a shop that had a Retina model for testing, but it was limited in applications that customers could not try many apps on it. However, I managed to get a list of text so that it looks like a word processing application because I wanted to see how much of long text the Retina can take (whether it's OK for software development or not). Honestly, it looked like the retina cannot handle long text at all, at least when it is not in Safari. It falls down to scrolling at sub 20 frames I guess (in the editor). Working hours a day with that machine would cause constant headache, at least for me. Other applications, besides iCal and Mail, worked very very smooth, no lags at all (Mountain Lion), not like on Lion back then.
My personal guess is that the CPU is completely overloaded with all the work to do for animations. Too many pixels to move in a too short period of time (not every animation is handled by the GPU). It looks like most applications draw their animations themselves, rather than using a software framework that supports GPU animations (something comparable to OpenGL). OS-supported animations seem to be very smooth all the time, like when a confirmation dialog pops up or something like that. But not those apps that draw their animations themselves. Therefore I would guess these issues can appear more often when the CPU is hot and gets throttled. But stuttering is also present when the machine is not hot, it's just much less noticeable.
