summary
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Villains in anime aren't always completely wrong in their actions, there are some justifiable reasons for their behavior.
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Some villains, such as Scar and Itachi, show a different side to their evil deeds, challenging the traditional hero-villain dynamic.
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Despite being despicable, villains like Kyubey and Gendou Ikari have complex motivations that blur the lines between good and evil.
Villains are a staple in any story, providing an opposing force for the heroes and driving the story forward with conflict. They are also shocks that make the audience hate someone. However, the best villains are the ones that aren't completely wrong. After all, realistically speaking, few people are the villains in their own stories.

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Some of the best villains are villains only in the framing of the story, others are just despicable in their ways but have noble intentions. Anime, known for great characters, naturally has some great villains. And while most of them are vile, some of them are not entirely without morals, and some of them are more righteous than they seem. These are anime villains who had a point.
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Lady Iboshi and Iron Town
Princess Mononoke
If it's like Fern Gully, then the residents of Iron Town and their leader Lady Iboshi will be the obvious villains of their story who take over the land as humans and pollute it without regard for its health. However, in Princess Mononoke, it's not that simple. While Iron Town seems like the bad guys, it's clear that they just want to be able to thrive.
This puts them at odds with the forest dwellers, who want to eradicate human presence in the area, which Lady Iboshi doesn't exactly stand for. Although they initially do not know how to interact with nature without harm, this does not warrant their death.
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stain
Fullmetal Alchemist
One group's terrorist can become another group's folk hero. Scar is a serial killer with a deep hatred for the Amestrian State Alchemists who killed fighters and civilians in one night in a bloody display of extreme power, ending a stalemate to end the war with his home, Ishval.
Some would call him a zealot, but his actions are as logically justified as any act of revenge, given the destruction of his country at the hands of Amestris and its alchemists. The issue is that he's not challenging, even targeting Edward Elric, who wasn't even involved in the battle.
5
Itachi Uchiha
Naruto
Perhaps the saddest character in all of Naruto, Itachi is also the show's most patriotic character, committing fratricide in hopes of saving his village and little brother from the horrors of war.

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Ultimately, Itachi may not be a villain, no matter how terrifying he is. His goal was a peaceful world, even through bloodshed, which contrasted with his peace-loving nature. With all the power and skill he possessed, he was still a victim of circumstance, trying to make the right decisions when all his options were dire.
4
Lordgenome
Tengen Topa Gurren Lagan
The main antagonist of the first season, Lordgenome, is presented as a tyrant with a callous disregard for life who orders his army of Beastmen to keep humans underground for no reason. Except, aside from the revelation of the Anti-Spirals and their ultimatum to keep the human population down or face extinction, the Lordgenome's order to put humanity under the dirt makes sense.
Although he could be kind about it, in Gurren Lagann the human soul is shown as a power of its own, meaning that in order to keep humanity around, he must crush their will to avoid the wrath of the Anti-Spirals. His ultimately good nature finally shows when he sacrifices his daughter and all of humanity in the final battle against the Anti-Spiral.
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Kyubey Puella Magi
Madoka Magica
Make no mistake: Kyubey is absolutely disgusting. It is part of an alien race called the Incubator, who act as familiars to the series' magical girls, granting them will and magical powers, as well as tasking them with fighting bloodthirsty witch monsters.

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In fact, witches are literally the end of every magical girl's life, a product of terrible despair. It is a system presided over by Kyubey, which exploits and abandons young girls in the name of creating energy to resist universal entropy. While their goals are good in theory, their methods are monstrous. But how do you deal with something as all-consuming as entropy?
2
Mewtwo
Pokemon: The First Movie
While Mewtwo is definitely the villain of this film, the reasons for his aggression make sense. After all, who wants to wake up, essentially alone in the world and said that you are an instrument of violence. Although his initial impulse wasn't exactly a good idea, especially when he bent over what he wanted her to be, striking out is a very reasonable response.
Eventually, he realizes the error of his ways and leaves with the clone Pokémon, saving them from the fate Giovanni designed for him and allowing them to live in peace. After Ash sacrifices himself, all future appearances by Mewtwo are as good guys, even if it doesn't seem like it at first.
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Gendou Ikari
Neon Genesis Evangelion
Let's get this out of the way: Gendou Ikari is a horrible person, maybe one of the most reprehensible in anime, and the worst father this side of Shou Tucker. He uses and discards people at will, has no regard for human life, and is cruel to his own son.
But he's the bad guy in a world where the bad guys win, no less than the fate of all humanity in a constant game of chess with the members of SEELE. Who can say that the ambition of wicked old men is purer than that of a man who wishes to see his wife again? We know it's not good for him, but it's entirely possible that if it did, he'd make a world of happiness with his wife and son.

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