Kaguya Otsutsuki is the final main villain of Naruto: Shippuden. Her introduction completely flipped anything fans knew about the world of Naruto from the beginning.
Since the start of Naruto, Sakura was infamous for her anger issues. She was very rude to Naruto, often punching him over minor things. Sakura's exaggerated anger was so prevalent that many fans grew to hate her.
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.
Tobirama and his feelings towards the Uchiha clan are known to the entire Naruto fanbase. Tobirama is someone who invented some of the most advanced jutsus that shaped the Shinobi world towards the end of Shippuden. He was the legendary shinobi Hashirama's brother and was the second Hokage of Konohagakure as well.
Shikamaru is portrayed as a lazy character, unwilling to apply his prodigious intelligence; Kishimoto has noted that he likes Shikamaru due to his easygoing nature.
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.
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.
Kaguya Otsutsuki was an ancient deity who was responsible for the first flow of Chakra reaching human beings. One of the most powerful beings, as all the other Otsutsuki are, she is definitely someone who can beat Madara.
Pain is arguably the greatest villain in Naruto. When a villain makes viewers question the very good that they believe in, then they have successfully done their job as an antagonist. Besides his flawless character build, Pain's arc, the Pain Invasion arc, is generally celebrated as the apex of the series.
Ino is the weak link of her clan, owing to her low Chunin rank and her relatively young age. Ino, like Sakura, is a medical ninja, although her powers have never matched Sakura's. She was also obsessed with Sasuke, which caused a rift between the two.
Probably Shisui. Any non mainstream character that's isn't filler, but play an important role in the story doesn't have any haters. plus Shisui is like the Uchiha gone RIGHT.
Black Zetsu reveals that he masterminded and influenced all the events from the end of Ashura and Indra's era to the current Fourth Great Ninja War.
1) Danzo Shimura
Danzo Shimura was incredibly powerful but also the most cowardly Shinobi in the Naruto series. He operated from the shadows, controlling the members of ROOT and manipulating Konoha's state of affairs.
1 Kaguya Otsutsuki
She wields the Rinne-Sharingan, which is needed to cast the strongest Genjutsu in the entire series. With her Rinne-Sharingan, Kaguya can cast the Infinite Tsukuyomi over the entire world.
Who is the god of Uchiha? Indra Otsutsuki is revealed to be the creator/ founder of the renowned Uchiha Clan in Naruto. He was the eldest son of Hagoromo Otsutsuki (The Sage of Six Paths) and the elder brother of Ashura Otsutsuki.
Hashirama Senju
This one is a pretty obvious choice, but it's worth restating. The legendary First Hokage, Hashirama Senju was known as the "God of Shinobi" for a reason. He was the only one capable of defeating Madara Uchiha during the latter's early life.