A long time ago, Disney and Fox were in negotiations about acquiring certain properties. Fox, after all, has properties that we all want to see end up in the Marvel Cinematic Universe. But now it's official: Disney has acquired the movie and TV segments of Fox. This means future X-Men, Deadpool, and Fantastic Four movies will be part of the MCU.
Perhaps the upcoming X-Men: Dark Phoenix, Deadpool 2, and The New Mutants are excluded, but migration isn't unlikely, especially for Deadpool, whose first movie was a smashing success. It remains a mystery how these titles will fit into Marvel's massive movie library, or if the tone will be "Disney-fied". What matters is that the franchises are now in good hands. With the newly acquired assets, Disney now has the chance to explore these storylines.
House of M
The story focuses on Wanda, a.k.a. Scarlet Witch, who is starting to have mental breakdowns which unleash her reality-warping powers. The X-Men and the Avengers team up to decide on how to handle this situation. In a nutshell, this is almost the same exact plot line as Captain America: Civil War, just replace Bucky with Wanda.
Thanos is the biggest baddie in the Marvel universe. It's hard to sift through the list on who else could match him in sheer epic glory. Fortunately, there's Onslaught, who is the accidental product of Professor X and Magneto and is responsible for the death of multiple Marvel superheroes. It will take all the power of the X-Men, the Fantastic Four, and the Avengers to take him down.
Avengers Vs. X-Men
Why is it when our heroes face off against each other, it's almost always about one person? Civil War was about Bucky. House of M is about Wanda. In the case of Avengers Vs. X-Men, it's about Hope Summers.
We can't do Secret Invasion without mutants. Skrulls are shape-shifting aliens with an intent to conquer Earth, and have been doing so for years by replacing some of our superheroes.
In 2019, the MCU will release Captain Marvel, which will formally see the introduction of the Skrull Empire; so a Secret Invasion storyline is not unlikely. Not even Marvel's first family can deal with the Skrulls on their own, much less a Super Skrull.
When the Serpent broke free in one of Marvel's major storylines, mutants played quite a role. The Juggernaut along with some heroes became weapons of the Serpent across huge battles around Earth and sees the destruction of Captain America's shield. This storyline is quite plausible considering it begins with Tony Stark announcing plans to help rebuild Asgard on Earth.
Doom and cosmic beings
Victor von Doom is one of Marvel's greatest villains. He's far more interesting than the Fantastic Four and is pure evil; blending both science and magic to achieve his goals. He also happens to have one of the most interesting origin stories that shows why he has so much hate in him.
Aside from Doctor Doom, Galactus, a cosmic being who devours planets like a McDonalds' Happy Meal, can be a powerful new threat after Thanos. With Galactus, the introduction of the Silver Surfer and the Heralds are sure to follow. Which then leads us to....
Marvel's Annihilation storyline is the equivalent of Avengers in space. It's one of the biggest events that happen across the galaxy while everyone on Earth is drinking lemonade. Annihilation features the Skrulls, the Guardians of the Galaxy, Silver Surfer, and Nova with the Nova Corps.