I flew ATA for the very first time, from MSP to MDW this weekend. Left on Saturday afternoon. Flew on 727's both ways. I was very pleased with how clean and refurbished both aircraft were, along with the seat comfort (I'm accustomed to NW's crappy 727's). The departing flight left the gate about 10 minutes late, but then we taxied about 20 minutes due to ATC delays. Got into MDW right at the scheduled time. I was impressed with the friendly and expedient beverage service, and they offered cookies AND peanuts as a snack - something NW doesn't do. (I don't think Vanguard does either - don't know about Air Tran).
The return flight last night departed over an hour late because the incoming aircraft from DFW that was to be our aircraft had to wait until a delayed flight to Boston pulled out of the gate. Boarding was pretty expedient once it commenced. Both outbound and inbound flights were full. Midway was absolute chaos. It's a complete mess. We initially went to the gate to check in but you couldn't even get close to the counter. So we went out to the terminal to check in at the main ATA counter. VERY long lines. When we finally checked in, the agent was very nice, and gave us seats (that reclined!) in the exit row, so we had tons of room.
Overall, nice service, nice aircraft. I'd fly them again, but I think until MDW is done, having a hub there is going to be a liability. Only minor complaint about the service is they seem to really like talking on the plane intercom, repeating the standard announcements more often than I've noticed on other airlines.