As a regular commuter on the shuttle, I actually really prefer to sit in back and usually do--I prefer to exit from the back. I also find that it's an unusual day when the shuttle is full...so I almost never have anyone in the middle seat. It was a little better on the MD-88s but still pretty open. The open seating is a hold over from the Pan Am Shuttle (which I first took in 1988) and actually works really well here. It's just so much easier to assure yourself an open row or sit with your buddies (yes, mornings contain a lot of regulars and I am not the only person who commutes from Boston to NY this way).
The flight time is generally 30 to 40 minutes depending on the landing approach. If we swing around to runway 4, it takes closer to 40 minutes but you get an awesome air tour of NYC (if you sit on the left side).