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The MCU has successfully created many intelligent, strong, and powerful villains since its inception in 2008. However, a lot of them are so evil that the fans love to hate them. A completely different case is those villains that come across as sympathetic despite the fact that they hurt the heroes or do multiple evil deeds.
The MCU took the care to give some of its best villains the type of backstory that makes the audience sympathize with them. As a result, some MCU villains became fan-favorites, and in several cases, they even switched sides later on and joined the heroes instead!
7 Bucky Barnes
Bucky is one of the most tragic figures of the MCU because when he commits atrocious deeds as the Winter Soldier, he has no control over himself. Brainwashed by Hydra, Bucky does what his masters want him to do, and it takes a lot of courage and pain to break free.
The Falcon and the Winter Soldier focuses on Bucky struggling with everything he's done and trying to make amends. Of all the MCU villains, Bucky is one of the most sympathetic ones because he never wanted to be a villain in the first place, but the Hydra stole his life and made him kill even people who once were his friends (such as Howard Stark).
6 Nebula
Karen Gillan's Nebula is one of the characters who started out as an antagonist and later went on to become a hero. She even took on Thanos in Avengers: Infinity War (2018) and helped the team in Avengers: Endgame (2019). Nebula was raised by Thanos, but her childhood was far from idyllic. She had to compete with Gamora all the time, and every time Nebula lost, Thanos replaced a part of her body with an artificial one which caused her a lot of pain.
Nebula's known true agony, and her initial bitterness and anger make sense in the light of what the audience knows about her past. However, Nebula eventually proves that there's much more to her and goes on to become one of the most sympathetic former villains of the MCU.
5 Helmut Zemo
Baron Zemo is the ultimate proof that even a villain with no special powers can succeed in his plans. Zemo manages to drive the Avengers apart in Captain America: Civil War (2016) and revenges the death of his family in the process. What makes Zemo sympathetic is that the audience can understand his motivations.
Zemo is driven by the loss of his loved ones, and won't stop until he feels like he avenged them. The sadness that Zemo emanates every time he appears in the MCU combined with Daniel Brühl's strong performances ensures that Zemo is one of the fan-favorite MCU antagonists. What also makes him different is that he's able to recognize and acknowledge when he's wrong. Zemo hates all super-soldiers, but he still admits to Sam and Bucky that Steve Rogers was one of a kind.
4 Scarlet Witch
When the audience first meets Scarlet Witch in the MCU, she's one of the villains as she and her brother Pietro are helping Ultron. Over the course of the movie, though, Wanda realizes what Ultron really is and joins the Avengers instead. Some of her future actions could still be considered evil (such as taking control over the lives of Westview) but after everything that Wanda's been through, it's easy to understand her.
Wanda has lost her entire family in a senseless and brutal way. And just when she finally found happiness with Vision and the Avengers, the Avengers first fell apart and Vision then died in front of her - twice. All of that would be enough to hurt anyone, let alone someone as young as Wanda. In the end, though, Wanda does the good thing, she lets go of her fantasy life and returns to reality, no matter how painful it is for her to do so.
3 Ghost
Ava Starr, aka Ghost, is one of the major villains in Ant-Man and the Wasp (2017) who endangers the heroes multiple times. Despite that, it's easy to understand where Ava's coming from. Her powers cause her a lot of pain, and it's getting worse.
Throughout the movie, Ghost's one real motivation is to heal herself so that she wouldn't have to feel this type of agony. Once Janet van Dyne offers to help her, Ghost stops fighting the heroes, proving it was her pain that motivated her actions, not being evil.
2 Taskmaster
The question of who hides behind the mask of the villainous Taskmaster is one of the major mysteries of Black Widow (2021). And when the truth comes out, it turns out that Natasha's enemy Dreykov is even eviller than the audience originally believed.
After his daughter had been injured and presumed killed by Natasha, Dreykov transformed her into the murderous machine that the Taskmaster is, and controlled her actions. Dreykov shows very little sympathy for his daughter, unlike Natasha, who tries to help the suffering young woman in the movie's finale, even if it means she's risking her own life in the process.
1 Doctor Octopus
Multiple Spider-Man: No Way Home (2021) villains come across as sympathetic people in the end, including Sandman, or Lizard. But Doctor Octopus has the most space of them all to evolve as a character. Even though he initially attacks Peter, when he realizes that he's in a different universe, he starts helping the heroes instead.
Doctor Octopus is the first one who gives Spider-Man the chance to fix him, to separate the connection between him and his tentacles. At many moments in the movie, Doctor Octopus comes across as a voice of reason, and he will even be more sympathetic to the viewers who know his story from the original Spider-Man 2 (2004), where Doctor Octopus sacrifices himself in the end in order to save other people.