Marvel doesn't have a wide variety of talented minority/POC/LGBTQ+ writers, editors and other higher level consultants that fully understand how to write and discuss bigotry in a 21st century, millennial/generation Z world. Racism, homophobia and the like haven't changed that much, but the world is different from the Civil Rights era. Mutant politics feels quite outdated the way it is written. Though I should say, Hickman's ideas of tackling sexual freedom with the mutants is a novel concept.
Marvel is also addicted to 'hero vs hero' narratives, as well as having a major case of 'event syndrome' because they believe these things sell (and perhaps the numbers say so) and thus the X-Men/mutants vs Avengers/Fantastic Four/the world narrative is put to the forefront. There's also the idea of maintaining the status quo of the universe (which is a mainstream comics wide problem) which keeps things locked in a perpetual state of stagnation as opposed to any sense of change.
Fans on both sides and how they view the characters of the opposing fandom are part of problem. X-Men fans think the rest of the MU superhero community might as well be mutantphobic because of their silence and inaction, and now wider MU fans think the X-Men only care about mutant problems and are supremacists. Neither seem to get that this is an out-of-universe problem with writers ascribing to this narrative for stakes and too many 'offices' within Marvel and an apparent lack of communication between them. Storm is an active character in Black Panther's book, is T'Challa's lover, was written to be worshipped as a god amongst Wakandans (which some books will imply that they are anti-mutant), yet this relationship is not acknowledged (as far as I know) in X-Books.
The thing is, if Marvel and X-Books want to posit mutantphobia as a universe wide problem, then it should be treated as such from all sides, instead of one. Why have non-X-Book writers barely acknowledged its existence recently? Many main larger universe titles are quick to tackle hot-button issues like sexism, racism etc but the in-universe bigotry that is apparently rampant is never discussed? Likewise, why haven't X-writers bothered to address which non-mutants in the superhero community are allies to mutants?
However, mutants being excluded from the wider universe does affect them more negatively than fans want to admit. I'm surprised no one brought up how rights issues affected X-Men titles, the way mutants were written (I v X) and their visibility in other media (Marvel vs Capcom Infinite). Shutting mutants out may seem like a good thing in making their marginalisation make sense, but it hurts the brand. One could argue that the recent superhero movie boom of the last decade (starting from 2012) is not something the X-Men and mutants benefitted from. The rise of the MCU and Marvel-related media in pop culture also saw the X-Men dwindle in popularity. Only Deadpool benefited from this, despite all of them being Marvel IP.