As a side note, I've wondered when my friend will stop, because after about two decades of solid X-Men stories, including the Phoenix saga, the whole "God Love, Man Destroys" mutant prejudice, and then end of Claremont writing the X-Men, the book fragmented with New Mutants, X-Factor, and then God alone knows how many other spin-off titles.
This got me thinking. MHR has as their introductory adventure a re-telling of "Breakout," which is the first six issues of the New Avengers. For those who don't know the story, the Scarlet Witch had gone crazy and ended up killing the Vision, Ant-Man, and Hawkeye (two out of three of whom came back). Tony Stark, a little hard up for cash at the time and overcome with grief, dissolved the Avengers and everyone went their separate ways. "Six months later" a handful of very popular Marvel heroes were brought together to stop a massive jailbreak at the Raft, the supervillain detention facility near New York. The "New Avengers" were Iron Man, Captain America, Spider-Woman, Spider-Man, and Luke Cage (Daredevil made a brief appearance in there too, as did the utterly regrettable Sentinel). Wolverine joined the team after a couple of issues, making the New Avengers officially the Marvel All-Stars.
That's what happened in the comic books, but the RPG suggests putting in your own team instead to become the New Avengers, especially cherry-picking PC's from the list of heroes in the back of the book. "Breakout" works both as a comic book and as an adventure because it is a pretty pat team set-up piece. But substituting your own heroes means you are essentially playing in an alternative Marvel universe branching off from about ten years ago, before the Civil War, before the Initiative, before the current "Heroic Age."
So if "Breakout" is a good bring-them-all-together piece for the Avengers, why not do the same thing for Giant-Size X-Men #1? The old X-Men disappear, and Professor Xavier recruits a bunch of new mutants (the PC's) to become the new X-Men. It works, it has tons of built-in storylines that you can choose to use or not use. What I would really do is go with the "New X-Men" and then port it into the universe of the "Wolverine and the X-Men" cartoon series, since I think that series is a sort of pastiche of the past twenty years of mutant madness anyways.
And, you've got a universe without Weapon X, or the Phoenix, or the "Iron Age" of Cable/Deadpool/whatever. If you want, you can set the campaign in 1975 and have a little fun with the bell-bottoms and afros and post-Vietnam themes. I even considered bringing in the Phoenix Force, but having it inhabit another person, one who I think is tailor-made for hosting it.
I'd share it with you, but I'm saving it for a campaign that probably won't happen.