It's no secret that Marvel has a strangle-hold on the box office. Just look at the amazing records that The Avengers set back in 2012! They certainly know how to make movies, and they have an incredible collections of comics to use as inspiration. However, some storylines are highly unlikely to ever actually happen, even though they definitely should.
Age of Ultron
Yes, I know that Avengers: Age of Ultron come out in a few weeks, but other than the name,the comics and the movie seem to have little in common.
In the comic series, Ultron has reigned death and destruction across the world, causing the death of many superheroes. The remaining heroes, including Hawkeye, Spider-Man, and Captain America, have taken refuge underneath Central Park. They travel to the Savage Lands, and a group of them travel forward in time to confront Ultron. Wolverine stays behind, and he and the Invisible Woman travel back in time to kill Hank Pym before he ever creates Ultron.
We have already recieved a taste of time-travel with X-Men: Days of Future Past, but this is taking things to a whole new level. Wolverine is known as being a morally flexible anti-hero, but to kill a hero as loved as Pym? This certainly would even be a darker superhero movie than the actual Age of Ultron is shaping up to be. This could also be Marvel's response to The Flash TV show, where Barry is currently testing the limits of time-travel to go back and save his mom.
The obvious problem with this idea is that Marvel doesn't own the rights to Wolverine or the Invisible Woman, who are two of the most important characters in the event. That being said, Marvel ended up with a deal with Sony for Spider-Man, so just imagine is Fox ever came to terms with shared custody.
Avengers Vs. X-Men
Obviously this scenario also includes a deal with Fox, but it would be a masterpiece. With all the hype that Captain America: Civil War is getting, just think about how psyched people would get for a battle between two of the greatest superhero teams of all time!
The plot revolves around Hope Summers. A member of the Nova Corps travels to earth and warns about the approaching Pheonix Force, and when Captain America finds out he speaks to Cyclops about Hope. He believed that the Pheonix was coming for Hope, and he wanted to take her away to protect her. Cyclops didn't agree, and soon the disagreement turned physical. Avengers and X-Men fought valiantly before the Pheonix arrived. Iron Man tried to destroy the Pheonix, but instead it separated and possessed Cyclops, Emma Frost, Colossus, Magik, and Namor.
The "Pheonix Five" We're nearly unstoppable. The Avengers had to fight as hard as they could to take down the mutants one at a time, but every time one of the Pheonix Five would fall, the others would grow stronger. Eventually the Avengers had to look to Hope Summers for help to take down Cyclops before he becomes too powerful.
This battle would surely be more intense than the Civil War and Age of Ultron combined. We've seen the Pheonix in X-Men: The Last Stand, though that timeline was erased during the events of Days of Future Past. In the current timeline, the Pheonix has yet to make an apparence, and Avengers vs. X-Men would be a perfect time to do so.
Marvel Universe vs. The Avengers
This one is definitely a long shot. I am fully aware that there is a 99.99% chance that this will never happen, but it should, and here's why.
In this comic series, a virus spreads through New York, turning people into Savage cannibals, and of course the first person to be affected is Spider-Man. One-by-one, superheroes either convert into cannibals.
People love The Walking Dead. People love The Avengers. This would basically be a combination of both of them. Imagine a world where a savage, cannibal Hulk bites off one of Wolverine's arms.
Imagine a world where the Punisher has to put Captain America out of his misery.
Of course this would have to be a movie far down the road in Marvel's itinerary. Honestly, it's probably never going to happen. But just think about how awesome that would be.