Airtran is my favorite airline, so much so that I fly them even though they don't serve O'Hare Airport, which is just a couple of miles from my house. We either drive to Midway or Milwaukee, which is bit inconvenient, but once there, it's so much smoother than dealing with security & the sheer size of O'Hare.
I find their staff to be very friendly & helpful; I love that if business class is still available when it's time for online check-in, that you can upgrade for $69 a person. The upgrade includes 2 free checked bags (a $45 value) and free drinks. And if you've already paid for a seat, they apply that towards the cost. I think it's a no-brainer and do it every chance I get. At MKE, it also gives you access to the priority security line, which saved me once; I never would have made my flight otherwise.
I, too, worry about the changes that will be implemented once the Southwest merger is complete. But for now I will continue to book & fly Airtran.
P.S. I hear a lot that flight times are changed. I've never seen them vary more than 10-15 minutes, which doesn't bother me.