My wife's rMBP has this issue quite noticeably. Given she makes her living as a graphic designer, this is not just an annoyance.
Our visit to the Genius Bar resulted in a diagnostic test that showed that the display was "behaving normally" (which, of course, a diagnostic software with no external sensor would be able to saw) and though our Genius "knows what the Internet says" (we were taking an agreeable stance and hadn't even mentioned any expectations) they were not replacing these machines because we'd just get another of the same part.
His advice? "Change your workflow."
If this showed up in a matter of hours you could change your workflow. It shows up in a matter of minutes though. Most of the applications I use have static portions. Eclipse, Xcode, Photoshop, iPhoto, Safari, ... Switching from one full screen app to another and I can still see both.
The workflow change I can see is use an app, wait 30 minutes, then switch to another app or don't on any single app for more than a few minutes (just kidding, those is not feasible)
I returned my 3rd rMBP for refund. My suggestion would be ask for a full replacement (maybe you win the Samsung lottery), get a non-retina MBP or ask for a refund altogether since the machine is defective and they admit there is no fix. If they don't refund it, there's always the matter of credit card company protecting their customers. Amex is pretty good with these things and I think you get 90 days of protection. Apple can take the machine and refund you or they can just not get paid by Amex (similarly for Visa and MC).