Re: Retcon the CU
If it had been up to me to design the CU, or up to me to design the 6th edition CU, I would end up breaking it up into two lines:
Psitech Universe:
This is the timeline of Alien Wars, Terran Empire, etc. In this timeline there are psychic powers, discovered by western civilization in the 20th century (all those pulp stories about people going off and learning powers) but not at all strong or reliable until future centuries.
Champions Universe:
This is pretty much the superhero segment of the CU, except for the Metahuman Registration Act and the IHA and maybe Genocide. I would toss in a dystopian collapse/meltdown of the CU Earth to handle all those post-apocalypse comics, but eventually the CU Earth rebuilds and ends up back in space in time for Galactic Champions.
Mutant Universe:
This is probably one thick campaign setting book and probably that's about it. It sets up a 'pure' mutant campaign where all those with innate superpowers are mutants or at best experimental cyborgs and you have experimental robots and powered armor suits around as well. Alternate timeline from the CU, though crossovers are not impossible.
As I have stated elsewhere, the X-Men never fit into the Marvel Universe very well. They're more of an SF style concept or extreme Iron Age concept pushed into a Silver/Bronze universe. The Mutant Universe would be more SF-ish in tone, fewer costumes, more uniforms, more realistic consequences, etc.