Naruto has been one of the most controversially popular anime of all time. Maybe this is because of the long run of the show, of the diversity in all these characters and also the reasonable meanings behind almost everyone's actions. The storyline of every character makes one feel connected or sympathetic towards them. Here are some of the great villains who changed or even remained villainous that still are the most loved.
Being the closest person to the leader of the Akatsuki group, Pain and also being one of the disciple of Jiraiya, the legendary Sannin, Konan's powers are exceptional. Even though we did not get to see her true powers in the Pain Arc, we saw her full limit when she almost defeated Tobi( disguised Madara Uchiha).
Once again, a member of Akatsuki group, a puppet ninja who had a desire to be completely immortal, like a puppet gave a very likable experience. The back story of this character makes everyone sympathetic towards him.
The disguised Madara Uchiha who ultimately was the mastermind and the original mysterious leader of the Akatsuki group. As the face behind his mask was revealed, he turned out to be an old friend of Kakashi Hatake, who got involved with Madara's idea of infinite Tsukuyomi, after Kakashi failed to protect his friend Rin.
The very first villain Naruto's team comes across during their first mission. The thing that appeals fans is the more sensitive side of his and his relationship with Haku. Unfortunately, this all happens and they both die very early in the series.
My personal favourite character of this series was Oorchimaru, the first big antagonist of the series. His thirst of immortality requires him to acquire different bodies that are compatible for him to move into and he sees Naruto's friend, Sasuke as a fit body and manipulates him by promising to make him stronger.
One of the most sympathetic villains is probably Nagato, the leader of the Akatsuki. He founded the akatsuki with his two friends Konan and Yahiko. He was inspired to fight for attaining peace in the world when Yahiko dies. His ideology of having peace is to destroy people so much that they become aware of what real pain feels like.
Obviously, this character would be on the top of this list. Brother of Sasuke and a rogue ninja that killed his entire clan, first is shown as a badass akatsuki member. However, later in the series when he dies while fighting Sasuke, his reason to every sin he has committed is revealed and his love for his little brother, makes him the most loved and sympathetic character of all.