I kind of like the idea of starting with just The Mutants, about all the mutants cropping up in society and how they use their powers for good or ill; and then potentially the X-Men grows out of that. People already know the X-Men, so they could easily either skip the origin story, a la Spider-man, or go for a more drawn out introduction that changes things up a bit from the familiar origins (as First Class kind of did for its first half).
There's been a few X series that really push the mutant experience as a found-family, as in NYX, so there's a lot of space to mine outside of Charles forming a cadre of child soldiers to beat up his ex for him.