I'm not going to go into all the reasons why, but I always wondered why Beast wasn't made the headmaster of Xavier's in Charles absence. I realize that he's not the golden boy that Scott was, but that's refuted because Emma Frost is headmistress. He's obviously intelligent, and has one of the least complicated histories of the major characters. If anything, the only drawbacks would be the "Dark Beast" persona, or trying to "cure" his mutation, but those are old news right? Besides, they pale in comparison to all of Scott's problems.
If anything, I'd rearrange the X-Books to include the least amount of titles, while still trying to appease everyone. Involve the writers in a mutual discussion to keep the storylines tied together, and continuity straight. I see it as a home team, consisting primarily of the characters already established in Astonishing, not because of Whedon, but because they're mostly my personal favorites.
Then, an away team, like X-Factor, featuring B-, C-, or D-listers given desperately needed characterization, featuring a semi-rotating cast of characters on top of an established investigative team, Madrox, Rahne, etc.
A New X-Men: Academy X book, featuring the actual students, focused on developing the characters before they become injected into the Senior X-groups. Think of it as Degrassi with superpowers.
Finally, there's probably room for an Excalibur, Alpha Flight, or other third X-team, as long as they do not operate in the same vicinity as Astonishing or X-Factor. Or, this could be seen as series of minis, run one at a time.
As long as plenty of conversation between writers and artists occurrs, to keep everything straight, it would probably benefit the MU to see X-Men as a seperate entity altogether from the rest of their books because, while they technically take place in New York, the mutants tend to stay among mutants.
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You have some interesting ideas for heroes, Anubis, though the names seem overly hokey, unless that's what you're going for. I can see them working as a "classic" team from the fifties, but if you're going for a more serious book the codenames need work.