The elephant in the room that the comics haven't addressed (to my knowledge at least) is that the whole "Humans wiped out the Neanderthal" premise has been shown to be false by modern genetic studies that show the different strains as interbreeding and that Neanderthal DNA is present in a lot of modern humans.
https://en.wikipedia.org/wiki/Interb...s#Neanderthals
So, while I can suspend disbelief for my comic reading pleasure, I'd actually really like to see this addressed in the comics where it's not about two 'warring species' and how there already is evidence of mutant DNA in humans and vice versa... "we" (humans and mutants) are already more like one genetic species than not... and see where that takes the drama and in-story prejudices and such.