My suggestions:
Theme: Feared and Persecuted
I know people dig their heroics, but the O5 (Original Five) felt to me like a necessity, a response of a species that needed protecting instead of a group of superheroes. When you put the X-Men as a struggling minority fighting for acceptance is where they are best, and it brings the characters together. When the world outside is dragging obvious mutants across the streets tied to pickup trucks, you make all aspects of your fight (philosophical, physical, etc) that much more important. The Brotherhood believes that without action, mutants will be killed off, and the X-Men think too much aggression will put them firmly AGAINST humanity, and provoke a conflict nobody wants. Set the game in the pre-Onslaught Era (Good Old Cartoon Show, more or less) or Post 198 (Where all mutants were depowered by the Scarlet Witch and only 198 are left).
This makes the grid (either the Mansion or Utopia) matter, it makes the superheroes of the setting matter (what the fuck are THEY doing), it makes other characters matter (so few you can't really just say 'fuck off and die' even to your enemies), that sort of stuff.
Also, I like it, and that is VERY important.
Roster: Year Two
Let people write their own versions of Cyclops and Wolverine, for as long as they obey some pre-established notions written in the wiki. Stuff like 'Cyclops must be this age or older'' or 'Angel has been a Horseman by this point' and then general guidelines 'No player may erase family members of a character during CG as determined by Earth-616 continuity', stuff you NEED to make the game work. Stuff that will diminish the effects of 'Who is this OC living inside my favorite X-Men's character's body' and still allow for some creativity.
Villains: When To?
The Brotherhood needs work. They need a home, they should have a structure for RP that lets them have friends, family, lovers and rivals among the X-Men and RP between them should be facilitated. However, some villains should be earned, imo, by Storytellers who prove they are capable of providing RP for the grid on a consistent basis. Characters like Sabretooth, Mystique and Mister Sinister should either be plot tools, or taken by people who know what they are doing and will help the game. I am a huge believer in not closing any doors, and being meritocratic. If players go the extra mile, maybe the game should find some wiggle room to allow some experimentation.
Young X-Men
PLEASE do allow them. Mercury, Rockslide, X-23 are all great characters. I am not hot on OCs either, and I am much more prone to teach as Nightcrawler, Emma or Gambit if it is a FC student. I am not saying BAN OCs, but OCs need to understand they are fighting an uphill battle and not resent other players for it. It would be unfair to hate people for not liking OCs, as it would be unfair to ban OCs altogether.
Enough Talk, Lets Game!
Lots of talking! Is this game gonna happen?! Or are we just babbling here?!