The rMBP also has more ports, particularly two USB 3.0 ports, which to me is quite valuable as I do tend to use a lot of peripherals. The TB2 ports are a nice plus should I venture down that path.
The MBA also has two USB 3.0 ports. No difference there.
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You're not alone, it's a really tough choice and even though I've loved my Air's the last two years even I'm debating.
My biggest gripe about the retina is being forced into such a low resolution though, even lower than my Air (WTF). It's ok though, you can scale, but then this happens. Check my post here about major stuttering/lag on the 13" rMBP.
Could just be software related with Mavericks, but no way to know for sure yet, or if it's still partially a GPU issue with Iris. Luckily I have a loaded 15 rMBP on the desk as well with the 750M and Iris Pro which doesn't exhibit this issue when I scale it's screen.
Ah, that's really important to know. If I get the rMBP I'd probably be using it scaled. But this is bad news! Pushes me toward the MBA.