Was the fate of the Morlocks in that world ever mentioned? Because i just had to imagine them leaving the tunnels under New York after the death of the X-men and the victory of the super villains and instead becomming like the Nomads from the Cyberpunk RPG setting (see 2077).
A collection of nomadic clans traveling across the devestated remains of the USA in self maintained and modified high tech vehicles, offering their mercenary services to the various factions still remaining, when they aren't stealing and scavenging from them (also somehow their children keep being mutants).
It would both fit their nature as survivors, while also being an interesting contrast to their classic depiction. Going from people so afraid of how the world would treat them because of their super powers that they hide in tunnels, to freely traveling across the country, not giving a damn what the world thinks of them and openly displaying their powers as a proud sign of thei identity.
And of course there could be some story where OML works with some of them, but never staying because he can't feel at home with them or getting too much reminded to the X-men.