It's one of those "each to their own" discussion points. For me, this was never going to be a 'simple' choice. Fortunately, I could spend some meaningful time with either systems before making a selection. The path I took was a 13" MBA (i7/8/512) > 11" MBA (i5/4/256) > 12" rMB (1.2/8/512) > 11" MBA (i5/8/256).
I'm not a power user, but I like systems that are quick and snappy. I also get annoyed when there's a noticeable performance lag/twitch/'hicccup'. Those one-offs are acceptable, but the rMB had consistent ones. The MBA's did not. From various beachballs during browsing, through slow office (mainly outlook and powerpoint), to jittery app start/shutdown, the rMB was disappointing. It might seem strange, but I don't really have an issue with the MBA's screen. Sure, retina is great, but its not a game-changer (for me). I actually liked the force-touch trackpad and the new keyboard. Battery life was OK, and the port issue did not turn out to be a factor once I got an adapter.
There's this novelty effect that I needed to consider too. At first, the rMB felt great - size, form-factor, etc. all made performance secondary for a while. But when you use this everyday, and it's your main machine, and once the novelty wears out, you're starting to notice performance more and more. It's then when you realise the compromises in terms of performance, and that doesn't feel secondary any more..
I'm still virtually undecided on the merits of the rMB. It's pricey, but so is the BTO MBA. The main aspects - form-factor, trackpad, keyboard, screen, are great. battery life is OK, not great. It's the all-round "sluggish" feel in terms of performance that disappointed me.
The MBA is a very mature platform. I don't think you can go wrong with getting one, and sticking with it for a couple of years. Apple refurbs are a great way to pickup a higher-spec'd system at a good price. The rMB journey is just beginning, and I'm sure it will become the main platform for ultra portables at some point. When it does, I'll be ready.