It could be the village elders. They often have a lot of power and influence in the Naruto universe. If they believe Naruto is a potential threat or they have some ulterior motives, they could be the ones holding him back, thus acting as antagonists.
In some fanfics, it could be a foreign power. They might have spies or agents in the village who are tasked with keeping Naruto weak. This foreign power could see Naruto as a future threat to their own plans of invasion or domination, so they try to hold him back through various means, like influencing the village's decisions regarding Naruto's training and development.
Maybe some hidden rogue ninjas within the village. They might be working in the shadows to keep Naruto from reaching his full potential. They could be afraid that a powerful Naruto would disrupt their secret plans or expose their illegal activities in the village.
The main antagonists could be the original Naruto's friends and allies. Since this is an evil Naruto, people like Sasuke, Sakura, and Kakashi would likely oppose him and try to stop him from whatever evil plans he has in the past.
It could be a new group of rogue ninjas who have a vendetta against Konoha. They might be led by a powerful and cunning ninja who has a personal grudge against Naruto or the village in general.
The Akatsuki could be antagonists. They might see Kushina's return as a threat to their plans. Since Kushina is a powerful Uzumaki, her presence could disrupt their schemes related to the tailed beasts. They could try to stop her from reaching Naruto or even try to capture her for their own purposes.
A former acquaintance of Beckett who has turned to a life of crime could be an antagonist. They might have some old grudge against Beckett, like Beckett once reported them for something minor but it led to them having a really hard time, so now they want revenge by holding Beckett hostage.
The main antagonists in a 'Percy back in time fanfic' could be the followers of the Titans. They were numerous and loyal to Kronos. They would view Percy as an enemy since he is from a time when the Olympians are in power. Additionally, if Percy travels to a time when a powerful and evil demigod once lived, that demigod could be an antagonist. For example, if he goes back to a time when a demigod was on a path of destruction before being stopped, Percy's arrival might disrupt the events that were supposed to stop that demigod, and so the demigod would turn against Percy. There's also the possibility of some ancient sea monsters that were more prevalent in the past and were under the control of the Titans or other evil forces.
A jealous classmate could be a main antagonist. This person might be envious of Naruto's popularity and his ability to make friends easily. They could try to spread rumors or sabotage Naruto's projects.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
One possible antagonist could be a jealous noble from Naruto's own kingdom who feels that Naruto doesn't deserve the prince title. This person might try to undermine Naruto at every turn, spreading false rumors about him or trying to sabotage his diplomatic efforts.
Another possible antagonist could be a fellow inmate who has a personal vendetta against Naruto. Maybe this inmate was once on the wrong side of Naruto's actions outside the prison and now sees this as an opportunity for revenge. He could try to undermine Naruto at every turn, from spreading false rumors about him to physically attacking him when the guards aren't looking.
Another option could be Orochimaru. He has his own motives and is always looking for power. He could be the head of a powerful gang in the criminal underworld of the Naruto world. He would constantly be trying to capture Naruto or his friends to use them for his experiments or to gain more power over the ninja world.