So this is how I would introduce the FF & X-Men into the MCU. Now that Disney bought Fox.
First the FF.
This one is easy, the FF are there already, they just don’t have their powers yet. They are young and would not have been expected to fight alongside the Avengers. Reed knows Doom, but he disappeared after the events of AOU. During the events of A4 we a sign outside the old Avengers tower which reads “Baxter building coming soon” We will learn that Latveria and Sokovia were once the same nation. But after the events of WW1 or WW2, were split into two separate nations. During the cold war Sokovia absorbed Latveria, but with the end of the cold war. The country was split again. Like the real life breakup of Yugoslavia. Doom will reemerge at the same time the FF get their powers. Having unified the renamed Latveria under his iron rule.
Now the X-Men/Mutants.
In Iron Man 3 Aldrich Killian shows Tony and Pepper the “blank spot in Human DNA/Brain. This where the X-Gene should have been, but Marvel didn’t at the time have the rights.
Disney bought Fox a little late in the game, but there is time to add a few scenes into A4. Judging by the A4 set photos, there is clearly some Infinity Gauntlet [frick]ery going on.
( - The Avengers share a laugh, while discussing DC's latest Efforts.)
Stark looks different, is wearing a SHIELD uniform, and Ant-Man is there. So, it’s obvious that the Avengers will lose in A3. Only to return in A4 and use time travel to beat Thanos. Ultimately resulting in them getting their hands on the gauntlet. Which I think will go something like this.
It makes the most sense for Cap to be the one to use it. He has the most will power, and won’t be corrupted by the power. He will though be overwhelmed by the power, and the gauntlet is destroyed. The Avengers will have won, but this is now an alternate timeline. Which sends the power of the infinity stones reverberating through space and time. This energy release attracts the Celestials to Earth. Specifically, Ziran The Tester.
(note – In the comics it was Ogen the Prober who created the X-Gene. I’m using Ziran, he was there at the same time, and created the deviants. Looks better as well.)
This will be the last scene in A4. Showing Ziran the tester on ancient Earth. It’s millions of years ago, Humans are still evolving from apes. Ziran experiments on a large group of “Ape-Men”. Then releases them back to Earth. Allowing Humanity to now realize it’s full potential. The X-Gene has been created. That blank spot Killian found in the Human DNA/Brain, will now be filled.
Now for an after credits scene to set up Mutants in the MCU.
We are in central Europe, around 17,000 years ago. A child has just been born.
But she’s no ordinary child, we hear her people speak. It’s an unknown ancient language. Translated on screen with sub-titles. “What is she? Asks one of the tribal elders. Then we hear the dying breaths of the baby girls mother, “Selene, she is called Selene”. The babies eyes glow red, and the scene is over.
The first, and immortal Mutant, Selene Gallio. That way she can show up down the road.
Using the real first mutant right off the bat, will help differentiate MCU mutants, from the dumpster fire fox leaves behind. There will not be a bunch of mutants everywhere. This world would be a more post M-Day type feel.
( NOTE- When we pick up after A4, mutants won’t be largely known to the general public yet. SHIELD, and governments know they are real. But they really haven’t “arrived”, on the world stage yet. )
Then a mashup of the FF&X-Men logos saying Phase 4 coming soon. The way Marvel ends all their movies.