The idea came to mind when I remembered how the MCU takes heavily from modern stuff both in 616 and Ultimate, and uses classic stories more in addition to it. Some that come to mind:
  • Iron Man's origin takes heavily from Warren Ellis' 2005 Extremis storyline (which was essentially a reboot of his origins to begin with), and a (very watered down) version of it was the plot of IM3.
  • The Incredible Hulk takes after the Ultimate incarnation where it's derived from the Cap's Super Soldier Serum, though also feature Gamma Rays as part of it.
  • The Avengers themselves, while characterized like the 616 version, was formed by S.H.I.E.L.D. like the Ultimates.
  • The Guardians of the Galaxy was based on the 2008 comic, as opposed to the classic sci-fi version.
  • Captain America: Civil War, of course, is loosely based on the 2006 Civil War event by Mark Millar.
  • Thor: Ragnarok is based on several modern stories including the 2012 Thor: God of Thunder, the 2013 Thor: The Mighty Avenger, and the 2006 Planet Hulk.
  • Black Panther is heavily inspired by Christopher Priest's landmark 1998-2003 run, and features several elements that came after that like Shuri.
  • Captain Marvel is based heavily on Kelly Sue DeConnick's 2012 run.

I think you get the point.

So when I look at the potential of MCU X-Men, and when I look at modern stories that could heavily influence it, what comes to mind is Joss Whedon's 2004-2008 Astonishing X-Men more than any other story. The reason for that being that Whedon's run was like a blend of both old Chris Claremont stories and new ideas from the modern age rolled into one. Like with Claremont, you had big adventures, superhero action, melodrama, alien invasions, and outside elements connecting to the MU, but like the modern era influenced by Grant Morrison and others, you had some of the darker tone, Xavier's School being an actual school for mutants, many characters introduced since Claremont, and an overall "updated" feel that the MCU would likely go for.

Plus, looking at the back of the trade, Whedon's run actually did sell itself as being a modernization of Claremont's stories.

I doubt Grant Morrison's run will be the base, due to it being very dark and the X-Men acting more as a strike team than superheroes, which doesn't quite fit what I imagine the MCU being. I doubt many other stories since will be an influence because many of them were mediocre at best. I also doubt we'll start with Hickman's run right away being the base, because the status quo is based off decades of continuity and having the mutants start with their own nation that's separated from others is less than ideal.

So that brings me back to Astonishing X-Men as the likely base inspiration. I was reading the entire collection the other day, and what I felt was that this could make a perfect baseline for the MCU to use when the X-Men debut. Plus, as said, it was written by Joss Whedon, who directed the first two Avengers movies and says he's on good terms with them now and is willing to rejoin, so there's a distinct possibility that Whedon might be the director. Who knows.

But that's just my thoughts. What do you think?