MCU Phase 4: 10 Biggest Challenges Facing Marvel Studios
6. Introducing The X-Men
Seeing as mutants were a thing in the comics timeline since before the birth of Christ, suddenly introducing them into a universe like the MCU is a tall order, especially when considering the X-Men would have assisted against the likes of Thanos were they around.
The most obvious solution to the issue would be to have the energy of the infinity stones create mutants. However, this would not allow for the decades long conflict between the ideologies of Magneto and Professor X to have existed beforehand, unless perhaps they were civil rights activists as humans.
Therefore, a much more convoluted remedy may be necessary. This could involve applying Wanda's "no more mutants" to the entire multiverse, meaning that the MCU's Earth only contains two or three hundred homo-superior that have managed to keep themselves hidden, or something else entirely.
Whatever the solution ultimately ends up being, it's an issue at this point in time.