The problem isn't Mutants being a new thing, the problem is that Xavier and Magneto's characters require both of them to have been around for a while before the X-Men.
They should pull a Captain America and have both of them have adventures in the 60s as the first Mutants (or perhaps only mutants) and then something happens that sends them to the future. Keeps them as having been around longer but also explains where they were in the intervening decades.
They should pull a Captain America and have both of them have adventures in the 60s as the first Mutants (or perhaps only mutants) and then something happens that sends them to the future. Keeps them as having been around longer but also explains where they were in the intervening decades.