I'd say the ultimate "Rogue Squadron" from the FreeSpace/Star Wars Universe would be Wedge, Alpha 1, Snipes, Luke Skywalker, Corran Horn, Gavin Darklighter, Mackie, Wes Janson, Derek "Hobbie" Klivan, Tycho Celchu, Myn Donos, and Pash Cracken
Rogue Leader (1): Wedge
Rogue 2: Tycho
Rogue 3: Hobbie
Rogue 4: Wes
Rogue 5: Alpha 1
Rogue 6: Snipes
Rogue 7: Mackie
Rogue 8: Myn
Rogue 9: Luke
Rogue 10: Gavin
Rogue 11: Corran
Rogue 12: Pash
Rogues 1, 5, and 9 are hard to pick because those are the Flight leaders, and you have to have Wedge be Rogue Leader just because he was for so long. I thought about making Corran 9 because he always was, but Luke needs to be at least a Flight Leader. Feel free to debate about my pilot choices...
EDIT: and Wraith Squadron has to be kept the same just because of their Commando abilities, plus the fact that they're just crazy as hell.