Originally Posted by
FUBAR007
Drop the continuity bomb, and start over...
...but not at the beginning.
Approach the franchise as "X-Men: The Next Generation." Broadly similar to Claremont's Genext, but much more expansive and developed. I'd retroactively place the times of the core X-Men we know--Xavier, Scott, Jean, Storm, Wolverine, etc.--around 15-20 years in the past and focus instead on their kids and their kids' peers. The history of this timeline would have some broad similarities to 616 as well as some major differences. The important bits of history would be fleshed out as needed as we tell the story.
The first core cast member we meet? A precocious, redheaded 15-year-old named Rachel Summers. She's hit puberty, and her mutant psychic powers are flaring up. Fortunately, her parents were prepared for that. It also doesn't hurt that they teach and live at the Xavier Institute. Retired from the X-Men, Scott trains new teams of X-Men, identifies potential leaders, and advises the current active team leadership. Jean is the head counselor at the institute's School for Gifted Youngsters under headmistress Emma Frost.
Xavier, meanwhile, is rarely seen these days, busy as he is running a network of dozens of Xavier Institutes set up across the world, each with its own covert X-Men team. (The X-Men's identities remain secret in this timeline.)
Magneto, Apocalypse, Sinister, Bastion--all long gone. But, new threats have risen to take their place. Mutants have gained a measure of acceptance in the world, but not in the way Xavier had hoped. Rather than seen as people with special gifts, they're viewed as commodities to be exploited. By governments, corporations, terrorist groups, organized crime. On the other side, newer, younger voices have filled the void left by Magneto. But, rather than attack humanity like he did, or covertly integrate like the X-Men, they're out and proud, demanding recognition and respect in the public square. And some among them refuse to take no for an answer. Still others nurture dreams of wiping humanity out.
As ever, Xavier and his X-Men find themselves smack in the middle, trying to keep peace in a world that doesn't want it.
Compared to the original franchise, the flavor of this version of the X-Men would be much more international and political to reflect current times. Less traditional superhero fantasy and more genre-blending action-adventure. Branch out into different kinds of stories: using mutant powers for scientific research and exploration, mutant crime drama, erotic thrillers with mutant powers, teenage mutant romance, mutant sports, and more. Endless possibilities.