The world of the Naruto franchise is populated by a lot of colorful characters. Though most fans are likely more interested in the Konoha 11 than anyone else, the series did feature a large number of interesting villains. No two villains were exactly the same, even when they had the same motivations or methods. A great number of the villains were even willing to be the bad guys because they thought they were saving the world.
The villains that populate Naruto's world aren't unlike the villains that populate the world of the Marvel Cinematic Universe. They have unique power sets, dabble in unsavory scientific practices, and hold grudges. When comparing the two, there would be some interesting counterparts in the two franchises.
Sasuke: Scarlet Witch
Sasuke spends a good chunk of the series as an antagonist when he decides to leave Konoha and train with Orochimaru. Sasuke, however, is completely motivated by the tragedy that informed his childhood.
Sasuke is the only surviving member of his family, much like Wanda Maximoff. Like Sasuke, Wanda seeks out power she thinks will help her get justice for her family. Sasuke goes to the one person his village considers the ultimate villain. Wanda goes to Hydra scientists and volunteers for them to experiment on her. They both leave the bad guys behind to help people in need, but they also both have more power than they know what to do with.
Kabuto: Aldrich Killian
Kabuto is a strange villain. He seems unflinchingly loyal to Orochimaru, willing to participate in whatever unethical experiments the latter wants to do. He also, however, turns on him when it becomes clear he can become powerful using Orochimaru's experiments as his own.
That's not unlike Iron Man 3's Aldrich Killian. Killian is the leader of a think tank before he becomes a villain. He's willing to experiment with whatever and whoever Maya Hansen needs to make her Extremis formula work. Killian even becomes a subject of her experimentation himself. When his and Maya's views no longer align, however, he shoots her in cold blood to use her work for his own power. Unlike Kabuto though, Killian faces some harsh consequences at the hands of Pepper Potts.
Gaara: Nebula
Gaara and Nebula both grow up in hostile environments. They become monsters as a result of the way they are treated and the weapons they are given. For Gaara, that's a tailed beast locked inside him that he can't control. For Nebula, that's pieces of machinery that replace more and more of her body as it suits Thanos.
Both begin to change when they are shown kindness by others who understand them. Gaara finds a kindred spirit in Naruto while Nebula finally starts to connect with her sister Gamora right before Thanos comes for them.
Orochimaru: Baron Strucker
If Sasuke aligns most with Scarlet Witch, it stands to reason that Orochimaru would line up with the scientist who wakes up her abilities. Though Orochimaru lives a relatively well-adjusted life in Konoha and is a formidable teacher to his followers, he becomes obsessed with how to increase power and how different shinobi abilities can be transformed or combined.
That's just like Strucker experimenting with the mind stone in Loki's scepter. Strucker pushes boundaries that he probably shouldn't, killing Hydra volunteers in the name of unlocking the stone's power. Orochimaru doesn't care who gets hurt if he's unable to lock secrets about shinobi power.
Konan: Ghost
Konan and Ghost are both victims of circumstance. A war leaves Konan an orphan, and despite learning how to protect herself with her two best friends, she loses one to more violence. That leads her to ally with the other, remaining unflinchingly loyal to his violence in the name of paving a path to peace and away from pain. Though she doesn't appear in many Naruto episodes, her story is a compelling one.
Ghost's pain is physical rather than emotional. She also loses her family, but in an experiment gone wrong. That also changes her. Konan's life is uprooted, but Ava Starr's whole being is uprooted as her body phases in and out of reality. She commits her crimes only because she wants to find a way to stop the painful process.
Hidan: Hive
Hidan might be one of the most memorable villains for anime fans simply because his presence in the storyline shifted the spotlight away from Naruto for a bit and onto Shikamaru. Hidan, functionally immortal, is the villain responsible for the death of Asuma Sarutobi. He's confident in his abilities, not worried about the possibility of death, and devoted to a vastly different religious practice than seemingly the rest of the shinobi world.
His time in the series calls to mind Agents Of SHIELD's Hive. The first Inhuman, Hive had a cult of worshippers devoted to him. He was also functionally immortal - at last on Earth. Just as Shikamaru had to take extreme measures to defeat Hidan involve explosives and buried body parts, the SHIELD team had to send Hive to space in order to get rid of his influence on Inhumans.
Danzō: Alexander Pierce
Leaders affiliated with a secret government organization who actually do more harm than good? That's Alexander Pierce and Danzō Shimura exactly.
Danzō is the founder of Root, which is essentially Konoha's Black Ops program. He has a reputation for being "dark," but the people in the village don't know just how power-hungry he is. Danzō manipulates events in his favor to try to take over the Hokage position, putting the entire village in danger. Pierce, on the other hand, is revealed in Captain America: The Winter Soldier to be loyal to Hydra. A high-ranking government official, he actually outranks Nick Fury over SHIELD. Both are men people trust with secrets that betray their respective organizations.
Madara: Red Skull
Madara Uchiha might not have had the same political leanings as the Red Skull, but the two did have a lot in common when it came to their desire to shape the world around them.
Madara, one of the founders of Konoha, lived in a time of great war amongst the shinobi. He simply wanted to find a path to peace but disagreed with his brother on how to achieve that peace. It led him down a dark path, one that included being able to "rewrite" his death and live much longer than he should have. Red Skull also operated during a great war. He also advocated for a world of peace, in a way. He wanted a "world without borders." Red Skull even lives on after his death, stuck on a planet as a kind of keeper for the soul stone. His teachings, like Madara, also live on, as Hydra continues in his absence.
Kaguya: Hela
One of a handful of characters in the Naruto universe whose abilities essentially make her a god, Kaguya is incredibly powerful, incredibly hard to beat, and someone who comes back from the dead for battle. That might bring to mind Thor's sister Hela in the MCU.
Like Kaguya, Hela isn't from Earth, but a planet far from it. Also like Kaguya, Hela's desire for power is what gets her in trouble in the first place. Hela ends up banished from Asgard, but returns to cause destruction, just as Kaguya is able to return to battle Naruto.
Pain: Thanos
Pain doesn't begin his life as a villain but as an orphaned child of war who watches the people around him destroy the world in a quest for power. Thanos is similar. Not always a villain, he desires to bring "balance" to the world. They both, essentially, want peace, but use incredibly violent means to achieve it.
While Pain uses avatars of dead followers to fight his battles, Thanos amasses the Infinity Stones and an army of followers. Pain eventually sees the error of his ways, but Thanos lives his life always believing his method is the best. Their ends are where they differ. If not for his fight with Naruto, Pain might have died in his belief that violence would lead to eventual peace.