Perhaps an over - controlling teacher who doesn't approve of Naruto and Sakura's relationship. This teacher might try to separate them by giving them a lot of extra work or by making rules that prevent them from spending time together. The teacher could think that their relationship is a distraction from their studies.
There could be a group of mean students who don't like Naruto because he's different. They constantly bully him and try to keep him away from Sakura. They might be the typical 'popular' kids who think Naruto doesn't belong in their school or around Sakura.
A group of troublemaker students might be the antagonists. They could be constantly causing chaos in the school, and Naruto and Sakura have to step in to stop them. These troublemakers might not like the new order that Naruto and Sakura are trying to establish in the high school.
One possible antagonist could be a popular girl in school who is jealous of Sakura's popularity and tries to undermine her at every turn. For example, she might spread false rumors about Sakura or try to steal her friends. Another could be a strict teacher who doesn't believe in Sakura's abilities and is always giving her a hard time, like constantly doubting her work in class or not allowing her to participate in certain school activities.
In a few fanfictions, it could be a jealous ninja within the village. Maybe someone who has feelings for Naruto and sees Sakura as an obstacle. This ninja could create a false narrative that leads to Sakura's banishment, thus becoming the main antagonist in the story.
In this kind of fanfiction, Gaara could start as an antagonist. He's the new kid from another school who transfers in. He has a very cold and intimidating demeanor. He gets into fights with Naruto and his friends because he has his own ideas about how things should be in the school. He doesn't trust easily and thinks everyone is out to get him. But as the story progresses, he could turn into an ally. Also, Danzo could be an antagonist. He's a strict, old - fashioned teacher who doesn't like Naruto's unruly behavior and tries to expel him from school at every chance he gets.
Often, it could be a group of rival students from another college who are jealous of Naruto and Sakura's skills or achievements. They might try to sabotage their projects or disrupt their college events.
It could be the Akatsuki members. Since they are often the main villains in the Naruto universe, they might also play that role in this fanfiction. They could be trying to stop Naruto from using his control over Sakura to achieve something that would be a threat to their plans.
Often, it could be a jealous classmate. Maybe someone who has a crush on Percy and sees Annabeth as a threat, so they try to create problems between them. Another could be a strict teacher who doesn't like Percy's carefree attitude and Annabeth's independent thinking, always trying to give them a hard time.
Often, Orochimaru can still be a main antagonist in these fanfictions. He might have some new, devious plan related to the Chunin Exams, like using the chaos of the exams to steal some powerful jutsu or secrets from the village.
It could be an original character created just for the fanfiction. Maybe a powerful ninja from a forgotten clan who has a vendetta against Konoha and targets Naruto, Sasuke and Sakura specifically.
Perhaps it could be the school bully. This bully might be jealous of Vegeta's strength and popularity among some students, and also of Bulma's intelligence and charm. So, he tries to create problems between them, like spreading false rumors or trying to sabotage their school projects.