I flew Airtran about two weeks ago between Atlanta and Milwaukee. My first time to fly with them and to pay for the seating. My son and I were flying together and wanted to sit together, so we did pay. At the time of making my reservation, I paid for and selected seats for all legs of the flight. I made my reservations on the Airtran website. As I stepped through the reservation process, it showed me a diagram of the airplane with the seats available for me to select from.
I didn't have a problem with selecting the seats, and we didn't have a problem with our seats being (un)available when we boarded each time. The flights both ways were absolutely full, with a number of people flying standby. Everyone was assigned a seat before boarding, and I didn't observe or hear any problems with seating on the plane.
All in all, MUCH better than the free-for-all for seats in the early days of Airtran.
I do not know -- however, there may be some seats that are not available for pre-selection online. Possibly they are available if you speak with an agent. I'm thinking that I did not see any of the bulkhead seats or any of the emergency row seats when I selected. But they may have simply been already taken.
Under the new seating policy, your seat will be assigned to you at one of 3 times:
(1) When you make your reservation, you can pay $5 per ticket per leg to get an immediate seat assignment. We gladly paid the $20 extra.
(2) Without paying the $5, you will get your seat assignment when you do an at-home check-in (up to 24 hours before flight time) and print your boarding pass from home or hotel or whatever.
(3) Without paying the $5, OR without printing your boarding pass at home, you'll get a seat assigned to you when you check in at the airport. If you've paid your $5, then you've got the seat. You are not required to print your boarding pass at home.
ONE TIP -- If you print your boarding pass at home, and if you are concerned about the possibility of someone being in your assigned seat when you board, then be sure to print duplicates of your boarding pass. When you board the plane, they keep the entire boarding pass for those printed at home. There is no stub for you to keep. They tell you to just remember your seat assignment. So if you want to be prepared to show proof of your seat assignment, then have that duplicate pass with you.
Oh -- And I have never encountered an Airtran employee who was rude. Airtran prides themselves on their customer service. You can bet that I'd take down a name and write a letter or email when I returned home.