Even after the merger, they operated as two seperate airlines. They couldn't use each other planes and such. Our flight from Bloomington, IL to Orlando was on Airtran, and not ex-Valu Jet. Later, they stopped the direct line so you would take Airtran to Atlanta and then ex-Valu Jet to Orlando. I believe on was called Airtran Airways and the other Airtran Airlines - anyways they operated totally seperate for quite a while. Airtran had a very good record prior to the merger - and haven't heard anything bad afterwords either.
I still try to fly American to get flier miles, but half of the time fly Airtran due to the pricing.
And yes, like ATA, Airtran has many new planes. Did have to fly ATA once out of Chicago since the prices were really high locally for some reason. Down to Orlando, I rode in a plane a week old. The next week we flew they said the plane was a week old. We said, wait, a week ago they said it was a week old. Guess what - it was a different plane that had been delivered a week after the other plane. Wow!