I have flown both many times, and much prefer Southwest. Why?
- I never have a problem with getting decent seats, even the one time we forgot to get on the computer (whoops!) and got "B" boarding passes - and there are 6 of us!
- Their change/cancellation policy is the best. It really helped me out last year.
- Airtran has changed my flight times numerous times, sometimes VERY drastically, usually without informing me. Southwest never does this.
- Oh, and everyone at Southwest is so nice!
All that said, I will still use Airtran from time to time if their prices are better. But if the itineraries/prices are comparable, I would go with Southwest.