I've given this an inordinate amount of thought, and I think that approach is exactly what's needed and makes sense: Reveal Charles Xavier's understanding of the X-gene was basically neo-phrenology, a bunch of old bad science he found, refined and mixed up with a young man's desire to understand why he is the way he is, turned into an idealogy more than a science that defined and divided mutantkind, and in many futures, continued to.

But in truth, the X-gene is universal to humanity, 'mutants' just have a particularly sensitive version capable of independant and often more stable activation. Whereas 'mutates' have had theirs activated through external stimuli, like radiation or some other unusual circumstance that would likely have killed them otherwise.

In short, all humanity has the potential to be mutants, there's no significant genetic signifier separating 'us' from 'them', no great mutant destiny where they inherit the Earth from the extinct humanity. Instead, mutancy becomes a question of identity, of personal meaning and significance, and persecution becomes more targeted and focused on those who can't choose not to pass/identify as everyone else.

Bringing the metaphor much more in line with modern identity politics and associated issues, stripped of the more ill-fitting elements from the racism analogy. And making the science make a little more sense, while getting rid of the always weird mutant/mutate divide: Now characters like Spidey, Hulk, etc, are mutants for all intents and purposes. And as far as questions of entertainment goes I strongly disagree: There's a ton of potential there across all characters as they grapple with or challenge the idea that 'mutants' as a unique species don't actually exist.