The problem with the problem (heh) of wanting a “coherent” line of development from where the X-Men were to where they are now is that they should’ve established Krakoa or at least adopted these ways of thinking years ago. Specifically right after Genosha a got blown up and not a country did anything. We see at the end of Rosencanny that things weren’t ever going to be the same. What that and the Age of X-Man did was present the X-Men, mutants’ greatest defenders, with the undeniable fact that they’ve kept throwing themselves at a status quo that would never see them as people. Not only that but they saw a version of paradise where they weren’t punished for their powers and even though they were faced with problems concerning expressions of love, some of the biggest pushers of Xavier’s Dream wanted to stay in a mutant-only world.
Back during Carey’s published works during Decimation, we have a notion amongst the mutant villains that they’ve always been at war with humanity. That alone wasn’t what made them villains, it was the lengths they took to present that fact. What the X-Men never acknowledged was that although they would protect humans (and by extension, human institutions) was that mutantkind was always at war. That simple fact was extrapolated into something that could finally unite mutants all over.