The majority of AirTrans flights have a stopover in Atlanta GA, as that's their "hub". What you really want to watch is the departure time and the arrival time ... for example, there might be 4 flights leaving Orlando, all connecting through Atlanta to one flight to Buffalo, so you want to book that latest flight that will still get you the same connection.
To check on the stopover, when you pull up the list of flights for your day of travel, there's a column on the far left beside the flight info that will say "1 stop" for example, click on it and it will give your departure/arrival times for all of your connecting flights for that total destination.
As well, AirTran is known to "change" their flight times on a regular basis. This happened to me last August, so our travel home ended up being an entire day, with many hours wasted at Atlanta airport. As for seats, service, etc, about the same as SWA, except that when you check-in online 24 hours in advance, you can pick your seats. Although going down last year, we checked in right at the 24 hour out mark, and the entire plane was full

and we ended up in the last row that seemed rather squishy and NO WINDOW ... it was like being in a closet.

For our connection in Atlanta to Orlando, we pretty much had the pick of the entire plane, so not sure what was up with that.
I would absolutely fly with them again, if the price were right. I prefer to get the n/s flight with SWA, especially travelling with the kids. And the DINGS yesterday and today seem to be going into mid-November now, so I'm still keeping my fingers crossed.
MaryLiz