So, obviously, Secret Wars will bring change to the MCU, and here are the main changes that I think we'll see pretty early on:

* The Fantastic Four have existed on Earth-616 for a while, and they are established heroes with existing relationships beyond what we'll see in Doomsday and Secret Wars, and the Baxter Building will be in NYC skyline. Also, they'll have two children.
* Doctor Doom will have a history with the other heroes and Reed Richards, but is not particularly villainous, just antagonistic towards them.
* The X-Men and Mutants have been established for a while, and they have existing relationships with the rest of the superhero community.
* Steve Rogers and Tony Stark now lead the Avengers from Mount Avengers, which is the hollowed out version of Tiamat's corpse.
* Steve Rogers and Sam Wilson share the mantle of Captain America.
* Norman Osborn is an established acquaintance of Spider-Man, who does not know his true allegiance, but is suspicious due to his history with the Norman Osborn of another universe.
Post Secret Wars changes to the universe theories