The most hotly anticipated addition to the MCU is easily the MCU in an X-Men reboot sooner or later, and it could be that their ing this late in the game will actually fix one of the biggest problems looming over their comic book counterparts. At the same time, however, this could also create an entirely new and equally significant problem for the MCU's mutantkind.
Having been introduced in 1963's X-Men #1, Stan Lee and Jack Kirby created the characters with the initial idea simply being to avoid having to explain the nature of their powers. It wouldn't be until later that the group developed into the allegory for prejudice and discrimination that they came to represent, appropriate seeing as the comic began its run in the heat of the American Civil Rights Movement and was originally canceled shortly after it. The characters really exploded in popularity under the penmanship of Chris Claremont, who was responsible for many of the team's most popular storylines, including Dark Phoenix (1980) and Days of Future Past (1981).
For all of their success, however, one criticism looms over the X-Men to this day. They don't make an abundance of sense in a shared universe with many of Marvel's other non-mutant superheroes, especially as so much of their story has revolved around their persecution. This is something that the group not being added to the MCU until now could potentially avoid. However, if the introduction isn't handled with care and meticulous attention to detail, then this late addition could make their lore unnecessarily convoluted, difficult to follow, and frustratingly confusing. Here's how.
Mutant Paranoia Could Make More Sense In The MCU
The X-Men and mutants ing the MCU at this stage could make the persecution of mutants less nonsensical from an in-universe context. Mutants have been an allegory for discrimination and persecution of "the other," almost since their inception. However, this status has never made a great deal of sense when considering that people in the Marvel comics universe are generally accepting of other clearly superpowered individuals who aren't mutants, even if they have no reason to suspect they aren't mutants. Even Spider-Man is an example of this as his low approval rating has almost nothing to do with his actual powers and is more about the variably successful smear campaign run against him by The Daily Bugle.
In the MCU so far, almost every form of antagonism civilians have shown the Avengers has been based on actions, not powers. This was epitomized by WandaVision. Even before any of that, there was the Hulk, whose powers were never presented as being the problem so much as his volatility. That volatility is something that could be used to rationalize the mutant paranoia, however.
Assuming history isn't rewritten to include them, the mutants being a sudden and widespread phenomenon would already make people nervous as they're a complete unknown. Couple that with the fact that many of them will likely be incapable of controlling their abilities, and the conditions are there for a climate of fear that leads to the inevitable discrimination of mutants. This is where the Mutant Registration Act could come into play as perhaps an even darker version of the MCU's Sokovia Accords. The Mutant Registration Act may not be directly based on the Accords, but inspired by them on principle and taken in an even more Orwellian direction.
The MCU's Avengers Would Have Good Reason To Avoid The X-Men
If the X-Men are new, it would likewise further explain the reluctance of the Avengers and others to help them with anything that isn't expressly a clear villain or threat. If the X-Men are persecuted by the MCU's version of the Mutant Response Division (MRD) or Sentinels, then the Avengers may wish to avoid another political incident by interfering. This works less well in the comics, as the Avengers have fought alongside the X-Men on several occasions - particularly against evil or extreme mutants like Apocalypse and Magneto - and know them to be heroes.
The Avengers may choose to actively stay out of conflicts between the X-Men and the MRD - a government institution - if only to stay out of trouble, especially for this new breed of superpowered individuals who are an unproven group. As the Sokovia Accords were never officially repealed, any and all Avengers activity that's not authorized by the government is technically still illegal. Post-Avengers: Endgame, the Accords have conveniently been ignored in a world that's largely proven how ineffective they are. Yet they still exist as an avenue for the governments of the world to smack the Avengers - and any other enhanced individuals down if they do anything the government deems extreme. Even if the MCU didn't want to introduce the Mutant Response Division, recent projects like Ms. Marvel have shown that the Department of Damage Control is being set up in a way that it could operate in live-action much like the MRD in the comics.
The Mutants' Introduction Could Break The MCU Timeline
The danger of adding the X-Men so late is that they - and mutant-kind, in general - have a long and winding history, both in the comics and in the Doctor Strange in the Multiverse of Madness, but as a version of Professor X different than any seen in live-action yet.
He, along with the rest of the Illuminati, were wiped out in Doctor Strange 2, but his introduction implies the presence of mutants, even if they're not on Earth-616 yet. If a different version of Professor X is retconned into the MCU - presumably alongside other older mutants like Magneto - then there'd have to be an extremely good explanation as to how all of these mutants remained hidden for so long, especially Magneto. If the mutants are a known quantity at all, then even if Xavier was inclined to hide for decades, Magneto almost certainly wouldn't be.
If the retcon approach is taken, then a lot of explaining would need to be done in order to justify the absence of mutants during major MCU events, not to mention the absence of any major events centering around mutants at all. A great deal of fiddling with the timeline of the MCU would become necessary, running the risk of making the lore daunting and virtually impenetrable. However, the setup of Multiverse of Madness offered a simpler way that the X-Men can be integrated into the MCU.
How The MCU Can Safely Introduce Mutants
The MCU needs to introduce mutants to the multiverse without fiddling with the timeline too much, while also explaining away mutants that are older, wiser, and more experienced, such as Professor X, Magneto, and Wolverine. The optimal way to accomplish this is through the Secret Wars. Doctor Strange in the Multiverse of Madness already showed that certain individuals can cross from one universe to another, for example, from Earth-616 to Earth-838. The post-credits scene showed that the multiverse is in peril, however, with incursions–or the collision of universes–happening all over. It's possible that multiple universes, including Earth-616 and Earth-838 (or other universes where mutants exist), could merge through events similar to the 2015 comic book storyline.
In order to explain the older mutants, some of the mutants in the world could be variants, brought over from another reality. This would be especially useful for the likes of Professor X and Magneto, as their own histories could remain intact without conflicting with the MCU. It would also prevent having to see the origins of several veteran X-Men who audiences would already be familiar with, especially as the early days of the X-Men were already very covered in Fox's X-Men movies.
At the same time, such an event could also bring the mutant X-Gene over to the MCU or, if it's there already, simply activate it. This could easily explain the presence of several characters already in the MCU who should be mutants, such as the Scarlet Witch. Even the supposed first mutant of the MCU - his Ursa Major mutant powers simply hadn't activated because the X-Gene was dormant in the MCU, leaving it to activate after the convergence of the multiverses. Whatever Marvel decides to do, bringing the X-Men to the MCU at this point will almost certainly solve the issue of their being so out of place in a shared universe if handled correctly.
