In 2011, Fox looked into making a crossover film that would have pitted the Fantastic Four against the X-Men. What little is known about the film indicates it would've been Fox's attempt at adapting Mark Millar and Steve McNiven's Civil War, and a post-credits scene would've then teased Secret Invasion, bringing the Skrulls to the big screen years before Captain Marvel.
Ultimately, the film didn't get made because X-Men: First Class succeeded. However, had Fox's Fantastic Four vs. X-Men movie been made, it would have been a colossal misstep for a number of reasons. In fact, it might've been even worse than Josh Trank's reviled Fantastic Four reboot, because it doesn't seem to get what's appealing about the team.
The X-Men films aren't light affairs, as they typically deal with themes of systematic oppression and violence. At their darkest, audiences watch scenes depicting genocide. By comparison, the Fantastic Four are very uplifting characters. The Tim Story films, which were the only Fantastic Four movies made and officially released up until 2011, are uplifting. They aren't particularly good, but they definitely aren't dour. Fantastic Four vs. X-Men starts with the Human Torch blowing a hole in Manhattan as he tries to catch Molecule Man, killing lots of innocent people in the process. This would have been a pretty dour way to start an FF movie and led to calls for superhero registration.
The conflict would have escalated, resulting in a scene in which Mister Fantastic pins Wolverine down and cuts off the mutant's arms with his own claws. The fight sounds outlandish and excessively violent, which certainly isn't a compliment. Reed Richards is a scientist. Even at his worst, he always addresses problems from a scientific perspective and with creativity. While the Civil War comic shows Reed at his worst, he's only at his worst because he seemed detached from humanity, not because he's a bloodthirsty maniac. Reed dismembering someone is very out of character, and it seems as if the script only wants to explore how to make his powers cool and gritty.
Although we've only got information about a few choice scenes, what we do know feels like spectacle trumped the logic of the script.
Is This the Right Story for an X-Men/Fantastic Four Film?
The original Civil War comic focuses on a conflict between heroes over superhero registration. After a terrible disaster involving the villain Nitro, SHIELD demands superheroes register under government authority so as to function as a paramilitary branch. This is in order to manage and organize heroes to minimize collateral damage. However, those on the anti-registration side argue this system is unjust and infringes on their rights and freedoms. Reed Richards plays a huge role in the Civil War comics, but the rest of the FF mostly sits things out. The Thing hates the conflict so much he just goes to France for awhile. Johnny Storm and Sue Storm end up siding with anti-registration, though they don't do much in the story otherwise. The X-Men are also pretty absent due to the fallout of House of M and other extenuating circumstances. However, registering with the government definitely has shades of the Mutant Registration Act, so it's not at all shocking the X-Men leaned towards the anti-registration side.
The story, which was adapted for Captain America: Civil War, isn't really a Fantastic Four or X-Men story. The problem is this: Civil War requires two idealists on the opposite ends of a spectrum. Iron Man is an industrialist billionaire living with feelings of guilt from the deaths of people due to a lack of oversight. Captain America is the embodiment of freedom, and is willing to stand in opposition to systems he sees as unjust. They're on opposite end of the spectrum.
Reed Richards and Professor X, though? Reed explores the wonders of science, while Xavier fights social inequality. These aren't polar opposite perspectives, nor does either perspective lend itself well to the core conflict of the original story: freedom vs. oversight. This makes the conflict mean less.
Adaptations definitely make changes, but here's the thing: the Mutant Registration Act is part of the Fox X-Men films. So naturally, the X-Men would be anti-registration. Because the film would pit the X-Men against the Fantastic Four, that means, logically, the FF would have to be pro-registration, with their motivation likely being guilt about the deaths of people in Manhattan.
In the comic version of Civil War, the conflict affects all super-powered people. But in a film with only the Fantastic Four and X-Men, the conflict is between a team of superhero scientists and a team of mutants. Problematically, mutants exist as a representation of different oppressed minorities, which is where the trouble with the potential narrative starts to show.
The X-Men films and comics deal with mutant registration. The villains, who hate and fear mutants, oppress and restrict their rights. William Stryker, Senator Kelly and Bolivar Trask are examples of this. The problem with the Fantastic Four vs. X-Men movie is that, in order to manufacturer conflict between the two teams, the former group will have to support a political opinion that will hurt an oppressed social minority. That automatically puts Reed and his family on par with those aforementioned villains. Even if the rest of Reed's team switches sides like in the comics, they still supported laws that would strip an already oppressed minority of their few remaining rights.
And let's not forget that the reason the conflict starts is because the Human Torch messed up. That means mutants would be held accountable for the actions of more privileged heroes. So not only would the Fantastic Four be responsible for the oppressive legislation, but they then, presumably, would force that oppression on innocent mutants who did nothing wrong in the first place.
Civil War as a story works when each side makes good points and audiences can understand the logic of both sides. Adding mutants in muddies that, because they're understood to stand in for different oppressed groups. When one side is suggesting the US Government further oppress an already oppressed minority, it's hard to see both sides.
There is no way the Fantastic Four can walk away looking like the good guys in this scenario. And fun, exciting adventures are the core of what make the stories about the team enjoyable. The burden of US law shouldn't be put on a team who spends half its time fighting in the Negative Zone or figuring out how to stop Galactus. The Fantastic Four vs X-Men film just feels wrong.