They just add them. No dacning around the issue. Fantastic Four are easy, just ignore the previous films, start again. X-men are harder however. The X-men and major characters are established in real world historical events. WW2, Nam etc. Their plight, hate and feared for who they are, is something they need to handle well.
It's funny as the idea that mutants have always existed doesn't seem right as in Marvel they are a big contention and always will be. They, to readers, represent persecution about being different, why Marvel tried to make it out like Inhumans were this I've no idea. Elitist community that chooses who it empowers vs just born that way and you have no control over it and are therefore hated... yeah. okay Marvel.
...plus, Agent Coleson said once 'telepathic abilities? there's no such thing.'
Has Xavier really been hiding mutants from the mass populace for so long? :P
Hmm, pie.
