Hey - I have flown both airlines and had a great experience on Air Tran last summer. I would consider them equal in terms of in-flight experience. The Air Tran planes we were on were new & clean, the people were nice, and the seats were comfortable.
They also offer satellite radio free of charge and if they have business class seats available at the gate they sell them for $50. We took advantage of that on our way home and loved it!
You can pay extra to pick your seats in advance, or you will be assigned your seats when you check in at the airport. (I think).
I have heard on these boards that Air Tran changes its schedules often, so you have to check in on their site every once in a while. Our flight for August did change by about 10 minutes.
I would say Air Tran and SW are pretty equal. I would not hesitate to book either of them for the right price.
Hope that helps.