Marvel Have Already Shown How X-Men Could Enter The MCU
2. What Agents Of S.H.I.E.L.D. Did
Though fans might've been forgiven for writing off Agents of S.H.I.E.L.D. shortly after its first season concluded, it's only gone from strength to strength since. The stuff involving the Inhumans, the Kree and various other elements of cosmic Marvel have all been received particularly well, and though Season 6 looks likely to be its last, the last four have all been stellar.
The show also introduced the Terrigen Mists the other year, with the Inhuman tech actually transforming Chloe Bennett's Skye into Quake, gifting her seismic powers. As in the comics, the Mists unlock the abilities of those with Inhuman heritage, with a dormant gene being reactivated by the cocooning process.
Though it may be apparent to begin with, there are lessons Marvel can learn from the Mists' appearance in Agents of S.H.I.E.L.D., and how they can incorporate the X-Men specifically. Both approaches would involve a generational divide of sorts, with an older group of X-Men having gone into hiding at one point or another, but both would involve the mutant gene having laid dormant for decades - thus providing Marvel with an appropriate explanation as to why no one's referenced the X-Men, the Brotherhood, or even mutants for as long as they have.
Now, the MCU could just as easily introduce another kind of mist - one that reactivates a dormant mutant gene - or they could expand further upon the lore of the Terrigen kind itself. Take inspiration from the comics, have the release of the mists act as the reason why there are no more mutants, and then have mutants reemerge gradually as the effects wear off.
Either way, it helps account for their absence and ensures that the mutant metaphor isn't lost in the process.