Some more stats from the DOT website
Mishandled bags (higher rank means less chance of losing bag)
SWA - 4
Airtran - 12
Ontime (for the last 12 months)
SWA - 5
Airtran - 14
Customer satisfaction
SWA - 1
Airtran - 10
So, if I want to arrive ontime, with my luggage and with a smile on my face, I generally take SWA.
I will fly whoever is more convenient, and out of Chicago that is usually SWA, but I will use Airtran when I have to (such as going to Atlanta).
As long as I get to Orlando eventually, it is all good.