I can understand what you mean about the seating arrangements with Southwest. You pretty much have to ensure that you're near a computer 24 hours before your flight so you can get on the plane first.
In terms of Air Tran, I found that the service/experience was onpar with other carriers, like Delta, United, and US Airways. I upgraded to the emergency exit the one time and found that made a huge difference. Regardless, it's still a standard experience.
With that being said...
My preference has always been for JetBlue. You do get a few more inches of legroom compared to the other airlines. I upgraded to the 38" legroom and, even though the space was great, found that it wasn't necessary the next time I flew with them. If you happen to get on the E90 planes (they have 2 x 2 seating), sit in rows 13 and up. They have a bit more space than the rows in the front. The A320s all have 34" of legroom, unless you get the upgraded 38". Oh...plus, you get a TV at your seat!