Can only comment about AirTran, have not used the other but we usually fly nonstop Airtran to WDW. I don't recall having my times changed, flight delayed, baggage lost or any problems, have always had good luck with Airtran. Prior to 9/11, had a poor experience with Delta sticking us on standby although we had booked many months in advance. Airtran was the one that got us home on both legs of our trip & we have used them since.
You can pay for your seats in advance for a little extra, after our issues with Delta the piece of mind it's worth the few dollars to us. Airtran also charges for checked bags but not carry ons. Have fun on your trip