Here is my pitch for how I would do over the current Marvel comics, or another AU like Ultimate.
In this new timeline, S.H.I.E.L.D. would be running the world mostly as a giant police state with it answering only to a few shadowy groups at the top. Nick Fury would be a large looming presence of the strongest man in the world, with various superheroes working for or against them in some capacity. The Avengers would be a core group made up of their best soldiers, the X Men being created from a combination of eugenics and mutation that have to deal with violent mutants that run wild rather than just Magneto.
The Fantastic 4 would be completely removed from the events of the world and end up in far away galaxies leading to more cosmic stories like Planet Hulk of them fighting tyrants on alien worlds
Tony Stark and Steve Rogers would be Nick Fury's personal bodyguards and would often clash over assignments where morality would come into play.
Thoughts?