I went with the 11" in the fall of 2011. The specs for the 13" model were announced here in Finland at the time, but no one carried it, they only had the 11" and I was too impatient to wait. However, I had browsed through many discussion threads like this one and seen many people not regret their decision to go with the 11".
At the time, I had a few months old PC with i5 running Win 7, which was my main machine, so I knew I wasn't going to be using the 11" Macbook as my main computer, just as a portable device when on the move. A few months later, after getting a taste of OS X, I ditched my new PC in favor of an iMac, and I am no way in hell ever going back to Windows now.
My concern with getting an 11" was that I had used an EeePC netbook with a 10" screen, and it had been a really unpleasant experience. Then again it ran Win 7 Starter... I went to an Apple store and they had a 11" Air and a 13" Macbook Pro side by side. The cost for these machines was actually the same, as they were trying to get rid of the Macbook Pros. I spent an hour with these machines, switching back and forth, and I noticed three things: 1) the SSD on the Air was significantly snappier, and 2) when I pulled up a web page on both machines, they both displayed the same amount of the content in spite of different screen sizes. And, lastly, the Air had a much better display - clearer, more crisp, better lit, and easier on the eyes.
I don't regret my choice of the 11" because the form factor is beautiful and painless to carry around, and the Core i5 is more than sufficient to power it.
If you're going to use the Air as your main machine and it will mostly sit on your desk rather than travel with you, go with the 13". If you want portable power, the 11" is a great choice...but bring a charger, because the battery's not the most long-lasting (unless you put the machine to sleep...the charge will last weeks).