The Marvel Cinematic Universe has expanded even quicker and more impressively than Ant Man does in Civil War. What began in 2008 with Iron Man has blossomed into a media juggernaut that pumps out at least three films a year, multiple TV series, and a multi-pronged Netflix brand. Perhaps that shouldn't be surprising. The MCU does, after all, rest on the shoulders of another media empire, Marvel Comics.
The MCU, however, greatly surpassed the popularity of the properties it's based on. Far more people have seen The Avengers than will ever read an Avengers comic. Hoping to cash in on this success, Marvel comics changed to match their films. It’s easy to see why they might do this. By borrowing from their wildly popular cinematic branch, they’re attempting to make the publishing branch more appealing to new fans. That being said, the level of subtlety with which Marvel has altered its storylines is definitely a mixed bag at best.
Quicksilver and Scarlet Witch are very complicated cinematic characters, since their movie rights are split between Marvel Studios and Fox. The versions seen in the MCU cannot be referred to as mutants or as the children of Magneto, since Marvel doesn't own the rights to those particular properties.
Thus, they ensured that the comic book versions would more closely resemble their iterations of the twins than Fox’s. First, they revealed that Magneto was actually not their father, thanks to a “family only” spell that Scarlet Witch cast, which affected Quicksilver but not Magneto. It was the Marvel equivalent of Maury Povich. Afterwards, the twins discovered they weren’t even mutants at all, but rather the result of genetic experimenting by the High Evolutionary. Take that, Fox Studios and also decades of continuity.
Perhaps no character has had their personality and history changed more than Peter Quill, AKA Star-Lord. In previous comic book continuity, Quill was a sarcastic and bitter veteran of countless intergalactic conflicts. As a survivor that had lost many friends along the way, Quill was known for being a dour realist and an excellent strategist.
That's a pretty far cry from the lovable, wise-cracking jackass who appeared in the Guardians of the Galaxy film. Marvel switched up their comic book version so that Star-Lord became younger and funnier, and they did so without much explanation at all. He was still apparently the veteran of all those brutal conflicts, but now he just had a sunnier disposition about it all. Hurray for logic!
Marvel Studios has managed to claw back the rights to some of its most notable properties, including Spider-Man, Ghost Rider, and Blade. The only two groups they’ve yet to win back are the X-Men and the Fantastic Four, both of which are owned by Fox. While the X-Men are too popular to ever get rid of, the same couldn’t be said for the FF.
This led Marvel to “de-prioritize” the team in favor of others that they actually held film rights for. Eventually, this led to the FF actually getting written out of the Marvel universe, when they became the caretakers of the rebooted continuity after Secret Wars. The world thinks that Reed, Sue, Valeria, and Franklin Richards are dead, but they’re actually exploring the multiverse and creating new worlds. All conveniently off-page, of course.
One of the most obvious differences between the early Marvel Cinematic Universe and the mainstream comic continuity was Nick Fury's design. The comic book Fury looked like a vintage David Hasselhoff, whereas the movie version was Samuel L. Jackson. That's pretty much as diametrically opposed as you can get within a species of mammal. Marvel corrected this discrepancy in an insanely ham-fisted fashion. They introduced Marcus Fury, Nick Fury's previously unknown black son. Oh, and he had basically the same military background, too.
The similarities don't end there, however. Over the course of the Battle Scars miniseries, Marcus lost an eye, shaved his head, and literally took on the name Nick Fury Jr. As a bonus, it turned out that Fury Jr.’s best friend was Phil Coulson, which brought the agent into the comic continuity.