Yes; Naruto has several good villains but most just end up having a change of heart. However, at the peak of their evil, it makes you wonder, the mental stability of the character. I will be examining some of the major villains here and now!!
Nagato - He was raised by Jiraiya and was on his way to become the "Child of Prophecy". However, corrupted by the hate the spewed after the death of his dear friend Yahiko showed his other side. He killed Hanzo in a cynical manner as well as all of Hanzo's Henchmen and most of Danzo's Root. All. He also killed
anyone and everyong who sympathized with the former leader. That is like the Soviet Great Purge and the Holocaust - this was mass genocide. He also fearlessly through Amegakure into a Civil War with no regard to civilian loss. Now comes the Invasion of Pain - he killed everyone who messed with him and wouldn't tell him where Naruto is. He was trying to kill Konohamaru proving he isn't above killing children and tried to kill a little girl and grandma, as well as Sakura and Kurunei. He wasn't above killing women either. He was immensely cruel at his peak of evil.
Obito - People underrate his cynicism. This guy slaughtered everyone who was present in the Death of Rin with the sole exception of Kakashi. And he showed no remorse either. During the Kyuubi attack, he showed no guilt when he abducted a recently born child and played with his life. He showed no remorse when he fought his former sensei and chuckled at the thought of killing Kushina after she survived the extraction. Next he went on to slaughter his clan. These were his family members. This included the elderly, women and children and he showed no signs of sadness after he did this. Obito used, yes
used Nine S-Ranking Nins. He, killed Torune by snapping his neck. Even Kabuto who is another extremely villainous character said "That was harsh." and for what? Just to test Kabuto's trust and skills. He showed no grief when fighting Kakashi his former comrade and continuously insulted the ninja and wasn't above killing him.
Orochimaru - Most of this is self explanatory. He conducted experiments on children..newly born children. He did this just on his quest for immortality and to learn all ninjutsu. 99/100 of his experiments involving Hashirama Cells died and Yamato was left as a probably damaged child. And what more? He grave robbed the likes of the most respected ninja in the world. He without shame attacked Konoha. Why? It's unconfirmed but it was probably either for Naruto (Kyuubi), Gaara (Shukaku) or Sasuke (Sharingan). He also without sorrow (debatable) killed his sensei. He was a father-figure to orphaned Orochimaru and what did he do? Murder him. He also killed an ally (Fourth Kazekage) because he served no use anymore. He used Sasuke so he can get a new fresh body and manipulated Kabuto just to serve him as a good spy. He attacked Itachi who was a fellow comrade for the same reason he used Sasuke. He wasn't above fighting children such as Naruto and Sasuke and essentially in a manner, ruined already scarred lives (Kabuto & Sasuke). He wasn't above fighting former comrades Jiraiya and Tsunade with killing intent. He was one of the most evil characters this series has seen.
Madara - He wanted to destroy the village he helped create. He wasn't above killing his best friend multiple times, during Pre-Konoha era and the epic battle between the two. He insulted the efforts of the 5 Kages and, without remorse made the situation harder and played around with the Five. He also with no signs of sorrow destroyed a whole division of ninja which probably encompassed thousands of shinobi. When asked about what happened to the Gokage, what does he say. "They're not okay.." He is one evil bastard. Not okay - you just screwed them over. Didn't say kill - not okay. He's evil and he wants to remove the Shinobi Alliance threat first. That includes like 40 000 ninja. And he formulated a plan to control millions of shinobi. If that's not evil, I can't fathom what you think is.
Sasuke - Coolest ninja ever and during the Five Kages Summit, one of the most evil. First, he rushes in a kills a countless number of samurai. Then he attempts to kill Raikage, Darui, Shee, Mei etc. Then he kills Danzo. He then without pity stabbed teamate Karin. He then fights Sakura - he was not above killing Sakura and what more? A Chidori to the face. He also engaged his former teacher and attempts to kill him multiple times. And then he tried to kill Sakura again. He killed his sensei cause he no longer served him any purpose and killed Deidara because he was
in the way. He killed Zetsu.. why? To test his powers. That's cruel.
There are many villains in Naruto. Just because they had a change of heart doesn't change the fact that they're still a villain and participated in, as proven, a countless number of evil acts.
