I got the base MBA and love it.
Couple things that informed my decision
Size/Weight. The 13" MBP/MBA models are the most popular because of their excellent size/performance balance. 15" computers are becoming a rather niche product as most people never need discrete graphics or quad core processing. The rMBP is lighter, but it is still feels like a MBP vs close to a MBA
Price $1199. I doubt most people will truly see $1000 worth of real world value between these the two.
Speed.
The rMBP is only 74% faster computationally than the base MBA under CPU load. This is significant, but will only be realized in CPU intensive very specific tasks. Graphically the rMBP is a beast, but again this only realized in GPU intensive tasks.
SSD. Both offer fast SSDs
Memory. Both offer up to 8GB. Few people need 16GB or 8GB for that matter. When the MBA came out, the base 11" only had 2GB of RAM. Not much, but was doable then (Core2Duo days) with the same OS, and now 4GB is standard across the bored with Ivy Bridge speeds. This is enough for Mail, iCal, Web, iTunes, and Office simultaneously. OSX/Core i-series handles memory very well
Retina. Non-optimized apps (most) are scaled to look like 1440x900, the native size of the MBA and non-rMBP, which lowers image quality. I don't think anyone is missing much until apps are updated. Even then I think photo/video apps would benefit more than anything. The Retina display on the iPad was met with similar feedback. I think the same will happen here. MBA is already hi-res due to the overall screen size.
Facetime. Both have HD cameras
Upgradeability. NEITHER are upgradeable (Practically)
USB 3. Both have
Thunderbolt. Both have
SD. Both have
Intel HD 4000. The graphical performance/power savings of the new IGP will primarily be realized in the MBA, as the rMBP will surely switch to the 650 every chance it gets. I recall my old MBP switching to discrete when running Chrome...
Really nice alternates. $1300 15" quad core Sandy Bridge refurb + $300 256GB Samsung 830 SSD + $100 8GB RAM = $1700. $500 less with 85% of the rMBP, while maintaining upgradeability.