The shinobi council or some of the elders in the village might also be antagonists. They might be afraid of Naruto's growing power obsession and try to stop him, either because they think he'll become a threat to the village or because they don't want to see the power balance in the village shift. They could set up obstacles for Naruto in his pursuit of power, making them antagonists in the story.
Sasuke can often be an antagonist in these types of fanfictions. Since Sasuke is also power - hungry in the original series, he and Naruto's quests for power could put them at odds. Their rivalry could be intensified as Naruto becomes more and more obsessed with power, leading to some epic battles between them.
Orochimaru is often a common antagonist in these types of fanfictions. He has a history of experimenting on people and his knowledge of jutsu could be used to brainwash Naruto. He might want to use Naruto's power for his own evil plans.
Often, ancient and powerful demons or dark gods can be antagonists. They might see Naruto's newfound godhood as a threat to their own power or plans. For example, a demon that has been sealed away for centuries could be awakened by Naruto's ascension and seek to destroy him.
Pain is often one of the main antagonists. Since in the original story, Pain was the one who ultimately killed Jiraiya. So in fanfictions where Naruto saves Jiraiya, Pain is a natural choice to be the bad guy. Another common antagonist could be Orochimaru. He had his own vendetta against Jiraiya and the Hidden Leaf Village. He might be trying to use Jiraiya for some evil experiment or to gain access to the secrets of the Sage Mode.
It could be considered somewhat common in the Naruto fandom. Hinata has a strong connection to Naruto in the original series, and fans often explore different scenarios in fanfiction. Her character has a lot of depth that can be further developed in these fictional works.
In some fanfictions, Naruto could be obsessed with power to prove himself to the village that once shunned him. He might start to overtrain and explore dangerous new techniques that no one has ever tried before. This could lead to him unlocking new forms of chakra, but also putting himself at great risk.
Danzo Shimura might be another one. He is very secretive and power - hungry. If Naruto and Naruko's time - traveling actions expose his dark deeds or interfere with his control over the village, he would become their enemy. He has many underhanded methods and a strong influence within the village that they would have to deal with.
The Akatsuki as a whole could be antagonists. In fanfictions, the Akatsuki might be interested in the power of Naruto's Evil Rinnegan. They could try to capture him to extract the power or use him in some way for their own goals. Pain, being a powerful member of the Akatsuki, could also be a specific antagonist. His own ideology about pain and peace might clash with Naruto's new, potentially more chaotic state with the Evil Rinnegan. Additionally, new original antagonists created specifically for the fanfiction could be common. These could be dark, powerful figures who are drawn to the power of the Evil Rinnegan and want to either possess it or destroy Naruto to prevent its misuse.
Often, Orochimaru remains an antagonist even in these fanfictions. His thirst for power and immortality makes him a natural foe for Naruto, especially when Naruto has new super powers to protect. Another common one could be Madara Uchiha, as his grand plans for the world are likely to clash with Naruto's newfound abilities and his desire to protect peace.
Yes, it's quite common. Naruto has a huge and diverse fanbase. The story's rich world, complex characters, and themes like friendship and perseverance attract many female fans. Fanfiction allows them to explore different scenarios, relationships, and character developments that might not be in the original story, which can be very appealing.
Madara Uchiha can also be a common antagonist in Naruto suffering fanfictions. He might be resurrected in a more powerful and malevolent form. His plans could involve directly causing harm to Naruto, either physically or by manipulating the people around him. Also, there could be new, original antagonists created by the fanfiction authors. These could be powerful dark mages or shadowy organizations that target Naruto specifically to further their own evil agendas.