Kaguya Ōtsutsuki is the overarching antagonist of the Naruto franchise.
Black Zetsu is one of the major antagonists in the popular Naruto series. He was the will incarnation of Kaguya Otsutsuki. He considered himself to be her third son. He was the villainous counterpart of the Sage of the Six Paths.
Kaguya is the mother of all ninjutsu. Obviously, she's the most powerful villain. Even though Kishimoto wrote her in at the last arc, as a character, she fits in with the mythology in the Narutoverse. Most of the techniques and powers used in the series are based on mythological beings.
Obito Uchiha is, perhaps, the biggest villain in the world of Naruto. Obito became a villain after witnessing the death of Rin at the hands of Kakashi. Convinced that the world of dreams was the way to go forward, Obito did everything in his power to help Madara achieve his goal.
He Wasn't Totally Evil
Though he loved the taste of his own blood and its noted several times that his chakra itself can be seen as evil, Madara himself wasn't a bad person — he just let circumstances in life lead him down an evil path.
Sasuke was stated to be the strongest Uchiha to ever have been born, including Madara. So, obviously, his powers do exceed Madara's. With his Choku-tomou Rinnegan and Indra's arrow, he is almost invincible. As a result, he is also one of the Naruto characters who can defeat Madara.
Madara Uchiha
As a brilliant strategist and a bloodthirsty fighter, Madara's influence reaches over many characters in the series, even though he died before the series began.
2) Obito Uchiha
The rogue Uchiha ninja's Mangekyou Sharingan ability alone gave him an incredible edge over Guy, who was unable to counter the technique with just taijutsu. Furthermore, like Kakashi, Obito is more skilled in all three facets of shinobi combat to the point of being able to be generally superior to Guy.
Not only was he nearly killed by the Fifth Mizukage, Mei Terumi, but shortly afterward, he was also almost turned to dust by Onoki using his Dust Release Kekkei Tota.
Although he changed his views mid fight in the fourth ninja wars, that would also cause his demise. In an attempt to save Naruto, Sasuke and Kakashi, Obito Uchiha sacrifices his own life and gets killed by Kaguya Otsutsuki.
Jiraiya. Jiraiya was an exceptionally competent shinobi, and he was the only member of the Legendary Sannin who could actually beat Itachi. He was trained by the Third Hokage, and learned how to use Sage Mode while training with the toads of Mount Myoboku.
With a tragic backstory and immense power, Kakashi Hatake had the classic recipe for a Naruto villain. Instead, he became a hero and Hokage.
obito uchiha (broken hero)
Gaara fights Deidara to protect the village, but is defeated. The members of the Akatsuki then kidnap him and extract Shukaku from his body. Gaara dies in the process but an elder from the village named Chiyo sacrifices her own life to revive him.
When the Akatsuki leader, Pain, invades Konoha, Kakashi engages him in battle, and dies from exhausting all his energy.
Sasuke is yet another strong character in the Naruto series who eventually surpassed Kakashi. Sasuke was so strong that he was able to perform jutsus like Indra's Arrow which has similar, if not the same destructive capabilities compared to Naruto's Six Paths: Ultra Big Ball Rasenshuriken.
Kakashi can penetrate most of Gaara's defensives jutsu, but the two have not faced off. Gaara's sand coffin is nearly impossible to escape, and Gaara has displayed the ability to square off against Sasuke with a semi-developed Susanoo. However, Kakashi is a skilled tactician and would likely be able to defeat Gaara.
kakashi will put up a very good fight but would lose to itachi like 7 times out of 10 he would win 3 times because of his performance against asura and deva path of pain who were the strongest paths of pain.
Itachi Uchiha has arguably the saddest storyline in Naruto. Itachi was initially depicted as a cold, heartless, and powerful warrior who massacred his entire clan simply because he could. He then left his baby brother alive and made him relive their clan's deaths via genjutsu.
Madara Uchiha
Sasuke aside, Madara is easily the strongest Uchiha in the land. His boldness knows no limits after we witnessed him directly challenge the God of the Shinobi in order to compare himself directly to the best. After obtaining the power of Rinnegan, he went on to control the Ten-Tailed beast's Jinchuriki.
Unfortunately, despite the Konoha leader's efforts, the series took a major casualty in Episode 218 by killing off its most powerful hero. While a lot of fans were concerned that Naruto died in Boruto, the sacrifice was actually made by the Nine Tails Demon Fox, Kurama.