Tough decision. I've got an 11" and my wife has a 13". I swapped a 15" MBP for an 11" MBA and don't miss the MBP at all.
If you carry your laptop around all day, or you spend a lot of time on planes, or simply like to surf on the couch or type away with your laptop on your . . . er, lap, then the 11" is ideal.
If your laptop spends most of its time on a desk, or you really need extended battery life, or you do a lot of photo editting on the go, the 13" is probably better. It kills the 11" battery-wise.
I chose the 11" because I needed a laptop I could take anywhere, anytime and work on the road. We have an external monitor and keyboard at home, so it doubles as a desktop. No problem there.
However, battery life is my biggest criticism of the 11" - if it had better battery life and a built-in sim card slot like an iPad for connecting to mobile networks, it would be the ultimate road warrior.