The X-Men are a great metaphor for difference - sexual orientation, gender, ethnicity, the ever-present divide between the generations. The concept of mutants as co-habiting with humanity and slowly taking over, however, won't be that far off.
Neanderthals are no more. As a genetically distinct species, they are extinct. Their cousins, homo sapiens, were better adapted, luckier or simply were more equipped to plan for their future - therefore, they survived.
That doesn't mean the substance of what Neanderthals were is gone; in fact, it's likely you've got a bit of Neanderthal in you right now. It's the same with ethnicities, languages, religions - there are no pure laine variants of anything out there right now. That which survives, adapts, which means absorbing the best of what's around you.
The purists have it wrong; you can't freeze time by fighting against that which is different - not if you want to survive in the long run.
Who we are now won't last, because it can't - that's not how nature works. 10,000 years from now, our descendants will be configured differently - they'll be as different from us as we are from homo sapiens.
Our time on this world is fleeting, but what we leave behind - and what, ultimately, we contribute to - carries on.