There are some minor differences which may/may not bother you between them that I noticed:
-The rMBP has the superior keyboard, although honestly, both of them aren't as good as the cMBPs. I personally think the Airs have the worst keyboards in any mac I have ever used, but that's just my opinion.
-They have comparable trackpads, but with the additional depth in the rMBPs, you get more positive feedback.
-The rMBP has superior speakers, but if you really cared about audio, you would have it hooked up to decent speakers/headphones anyway.
-It's easier to use 2 monitors with a rMBP than an Air, although, if you're using external monitors a lot, one might question why you need a rMBP at all...
I'm sure there are other differences as well that aren't obvious (dimensions/weight/battery life/etc.), but what it boils down to is: do you want the retina screen or not?m