Atlantis is the next scheduled to fly, and Endeavour after that. Just where they happened to be in the rotation, and which one they felt they could get flight ready first.
They are, for the most part, carbon copies of each other with some minor differences.
Of all the orbiters built (not incl Enterprise), Columbia was the most different. It had a lot of test equipment that the later shuttles did not have - most was for the first "test" flights of STS1-4, but it was taken offline in 1984 and 1985 and modified with some additional test equipment, which data from actually aided in the investigation into its demise in '03. The test equipment also made Columbia heavier than the other orbiters and thus less capable for some of the heavier lifting missions and ISS missions.
Some minor improvements were made to each successive orbiter, with the older ones being modified at various times.
Endeavour was built mostly from spare parts as the replacement for Challenger.
Atlantis and Endeavour both started out as all glass cockpits, while Discovery was retrofitted.
According to the Nasa web site, no orbiter was delivered with a glass cockpit. Atlantis was the first to receive the retrofit to the all glass display and the system first flew on STS-101 in May 2000. Columbia had been retrofitted before its last flight, and Discovery and Endeavour have been upgraded during the downtime since the Columbia accident.
Endeavour was delivered in 1991 with significantly improved avionics over the other orbiters, but it was not the current glass cockpit set-up.