Airtran uses 737's and new 717's, while I believe SWA is all 737's. SWA has no first or business class. I believe Airtran does have business class.
737's are 3 and 3 and IMHO, a tad more comfortable on SWA than USAirways...except for that infamous middle seat. 717's are 2 and 3 and the 2-seat side should offer more room although every airline configures things differently. I haven't flown AT, so can't comment on specifics or actual comfort level.