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For every Marvel comic book storyline that makes it into the MCU, there are dozens more in the comics that never appear in the movies. One reason is that they work with characters who aren't yet present in the MCU or have already departed it. But a similarly common option is that the comic book storylines would prove to be too much for the MCU.
Either they deal with controversial or sensitive topics that would trigger the audience, or they portray some established characters in a different, not so flattering light. Whatever the case, there are several Marvel comic storylines that are unlikely to ever be portrayed in the MCU.
6 Ms. Marvel's Traumatic Experience
Before she became known as Captain Marvel, Carol Danvers used the superhero name of Ms. Marvel that later went to Kamala Khan. During this time, Carol went through a traumatic experience when she was assaulted and got pregnant as a result. The whole story got even more bizarre from there on because of time travel shenanigans.
Even though the MCU introduced its first solo female-led movie only in 2019 thanks to Captain Marvel, it's difficult to imagine the people responsible would give green light to this story to appear in this MCU considering how it treats women. Overall, the topic is too sensitive, and the storyline is considered too controversial to ever become a part of the MCU.
5 Daredevil Kills The Kingpin
Despite everything that Wilson Fisk aka Kingpin did to Matt Murdock and Daredevil in the comics, the costumed superhero usually keeps a higher moral ground and wouldn't result to murdering his enemy. However, one What-If? scenario saw Daredevil kill Kingpin. Instead of taking him on in combat, Matt shot Fisk in the head.
Such graphic imagery is unlikely to appear in the MCU, considering it shied even from portraying Echo shooting Fisk (possibly so that it could bring Fisk back). Also, with Daredevil only recently appearing in Spider-Man: No Way Home (2021) for a brief scene, it's more plausible that the MCU will focus on integrating him further into the universe in a more positive, not so violent way.
4 The Hydra Captain America
In one of the more controversial comic book twists, Captain America was revealed to be a secret Hydra agent after the history had been changed by Red Skull and his allies. The MCU made a nod to the storyline by having Steve Rogers pretend he was a Hydra agent when he wanted to get Loki's scepter from Sitwell.
However, with Steve now gone from the MCU, it's highly unlikely the MCU will include this storyline since it's too extensive and would require bringing Chris Evans back. The best the fans of this comic book series can hope for is to see the story adapted in the animated What If...? series but it might prove too difficult to fit the story into a single episode considering its extent in the comics.
3 The Intimate Relationship Between Wanda And Pietro
With Pietro dying shortly after his first appearance when he sacrificed his life to save Clint in Avengers: Age of Ultron (2015), it's unlikely Aaron Taylor-Johnson will reprise his role. And even if he did, it's hard to imagine the MCU would choose to portray Wanda and Pietro Maximoff as two siblings who are much closer than a brother and a sister should be.
Incest isn't an entirely new topic in the world of movies or TV, thanks to the likes of Game of Thrones and Jaime and Cersei Lannister, but the MCU is unlikely to include it. Not only would it diminish Wanda's relationship with Vision and the love she had for him, but there's also never been any indication that Wanda and Pietro had any other than a sibling bond.
2 Deadpool's Relationship With Spider-Man
Deadpool has had multiple romantic interests in the comics but one of the people he liked to flirt with a lot and didn't hide his admiration for is Spider-Man. While a lot of fans would like to see Tom Holland and Ryan Reynolds team up in the MCU to witness the banter between Spider-Man and Deadpool, this is one aspect of their relationship that the MCU is unlikely to go for.
Not because of the lack of representation, but because of the age difference between the two characters and their respective actors. Spider-Man started out as a 14-year-old kid in the MCU and even though he's older now, he's still significantly younger than Reynolds' Deadpool so Deadpool flirting with the much younger superhero might not come across so well.
1 Gwen Stacy's Relationship With Norman Osborn
One of the most problematic comic book relationships is Gwen Stacy's affair with Norman Osborn. In the comics, Peter learns after Gwen's death that she and Osborn had an affair, one that resulted in Gwen getting pregnant and having twins. The twins later made an appearance to confront Peter. Not only did the fans think the storyline threw shade on Gwen's memory, but there was also the fact that Norman Osborn was old enough to be Gwen's father and that he also killed her later.
Not to mention that neither of these characters is established in the MCU, and if Gwen Stacy ever makes an appearance, it will most likely be under different circumstances, and not just as the girl who made the mistake of getting too close to the Green Goblin.