Air Tran has two types of aircraft: DC-9 and 717. The 717's are all very new (2 years or less) and the DC-9's are very old (like 30 years+), so it makes a big difference what type of aircraft you are on.
I have flown many times on Air Tran, mostly Atlanta-Orlando and Atlanta-Tampa. Usually things go smoothly. When they don't, the delays can be very long because they may not have a replacement aircraft handy. Also the gate staff usually have no clue how long a delay might last.
The $25 upgrade to business class is normally only available for full price tickets (which are still much cheaper than major airline full fares), though they sometimes have promotions where you can upgrade any fare.
As others have stated, seat assignments are made when you check in, so it pays to be early.