I've owned the 11" MBA (twice) so I feel qualified to offer an opinion.
First, although the dimensions appear very similar on paper, in real life - in your hands - the rMB is very noticeably lighter and thinner. Whether that matters is a different question, but if portability is important, it may be a factor for you.
The display is a huge difference. The MBA has never gotten an upgrade from the original TN panels that were so-so when first introduced and have made no progress since then. The viewing angles and color accuracy are poor, and calibration doesn't really fix this. Resolution may or may not be an issue as well. Yet another display issue is that the 11" is 16:9 vs. 16:19 for the rMB, which means you get maybe half an inch/12-13mm additional vertical display space, which is nice if you work with documents or spreadsheets.
I think the port issue is hugely overblown, but if you think you'll have a hard time managing with dongles, avoid the rMB. Personally, I don't see much difference between having a bunch of cords connected to a single cord vs. having a bunch of cords connected individually, other than the fact that unplugging the dongle is faster.
If you need the dongle while traveling, though, it could be a factor for you.
MagSafe is a sad loss but i have never had a laptop snagged on the charging cord, and neither have my wife or my two now-adult sons or any of their friends. YMMV, I guess.
The keyboard is different, neither better nor worse. I've had this rMB since Monday night and I've basically used to it. The setup at the Apple Stores is poor because the table height is horrible for trying to type, but you might want to visit an Apple Store and try it out in person.
In real life use, the performance of the Core M is for practical purposes as good as the 11" MBA. I don't do encoding or other long-term CPU intensive projects on any laptop; if you think you might, you might tilt toward the 11" MBA. Personally, for tasks like that, I use a desktop.
Configured "equally," they're only $100 apart in price - but it isn't really equal, because for the extra $100 you get one of the best displays Apple has ever put in a laptop. (See the Anandtech review.)
There is a caveat with the rMB: it is a first-gen machine and there is a big chance that it will be changed significantly in the next couple of product refresh cycles. If you're adverse to early adopter risk, steer clear.
TLDR: the 11" MBA is a wonderful machine crippled by a horrible display. The rMB is better in many respects and worse in none unless your are hung up on ports that you probably don't use. The rMB is a far superior machine for most people.
store. I was surprised at how tiny it actually was! To me it kinda seemed like an iPad with a mouse and keyboard. It's very nice.