Just because a character is technically a villain doesn't mean everything they do is terrible.
There are plenty of anime villains who were right, even though their actions were arguably evil. Some – like Sasuke Uchiha of Naruto and Scar from Fullmetal Alchemist: Brotherhood – were victims of state-sanctioned violence seeking justified revenge. Others, like Shougo Makishima of Psycho-Pass, tried to take down corrupt governments to potentially save thousands of lives, but inadvertently got their hands dirty in the pursuit of justice.
Anime villains who are pure evil can be fun, but when an antagonist has relatable motivations, the story is always more nuanced.
His villainous behavior began when he killed the Rockbells, two doctors who had been treating his wounds. The act was thoughtless, one borne of panic. From there, Scar went on to take the lives of Amestrian soldiers who he believed deserved to die for their complicity in the war.
Rather than letting revenge consume his life, Scar ultimately comes to regret his actions, as he realizes hate begets hate, and holding onto a grudge serves no purpose. While killing the Rockbells was clearly unjustified, it’s hard to fault him for going after soldiers, since some of his victims were directly involved in the Ishvalan extermination.
Stain Made Some Decent Points About Capitalism In 'My Hero Academia'
Despite being a vicious murderer, Stain is a villain with conviction. He despises professional superheroes, as he thinks they're hypocritical liars who care more about making money than actually saving people.
Stain wants to deconstruct a society that values money above people's lives, so he starts killing the pro heroes who symbolize the broken system. He's reluctant to hurt anyone who isn't a professional hero, and will only do so if he's physically threatened.
While his methods are questionable, Stain makes a good point; My Hero Academia's hero system is deeply flawed. The society's laws are convoluted, heroes don't always protect people who need help, and the whole enterprise is ruled by capitalism.
Killing the people who work for the hero system may not be the right away to get his message across, but Stain's actions do not invalidate his observations.
Lelouch is a nuanced character, so it's difficult to classify him as a hero or a villain. He commits some atrocious acts in the name of his goal, which include killing his half-sister, betraying his friends, and lying to his followers.
However, Lelouch's vision is laudable; he wants to free Japan from the iron grip of Brittainian control. Regardless of his methods, he is right to try and dismantle colonial rule.
Sasuke Uchiha is only a villain for a small part of Naruto, and he's arguably in the right the whole time.
After Sasuke realizes the Konoha government forced his older brother to murder their entire family, he's understandably furious. When he hears about the baseless rumors that were spread to justify executing his clan, he's even angrier. He defects from Konoha and declares a vendetta against its leaders.
When a governing power forces a 13 year old to slay their family, it's hard to think of them as the good guys. Sasuke had every right to be angry, even if some of his actions were a little too brash. While he probably shouldn't have attacked groups of innocent people, it's hard to definitively say what the right course of action was in a situation that's so horrifically messy.