Well, I think it's in terms of power. Omega, being the last letter of the Greek alphabet, is the most powerful. I've seen a numbering system too:
Class 1: Toad
Class 2: Jubilee, Gambit
Class 3: Cyclops, Wolverine, Storm
Class 4: Magneto, Xavier, Apocalypse + Horsemen
Class 5: Jean Grey, Iceman, Elixir
You get the idea...I just filled in the ones I'm pretty sure of.