Perhaps some of the jealous monster students who don't want Naruto to succeed in school could be antagonists.
There could be a powerful monster teacher who has a grudge against humans. This teacher could constantly give Naruto a hard time, for example, by grading him unfairly or making him do extra - difficult tasks. The teacher's actions would create a major obstacle for Naruto in his journey at the school for monsters.
It could be a group of traditionalist monsters who believe that humans don't belong in their school. They might try to drive Naruto out by setting up difficult situations for him, like making false accusations or trying to get him to break the school rules. These antagonists would add conflict to the story as Naruto tries to prove himself worthy of being at the school.
In a world where Naruto is a fish out of water, the local bullies or those who uphold the unfair traditions of the world could be the antagonists. They might oppose Naruto when he tries to change things for the better.
Well, it could be that Naruto has to learn how to interact with monster classmates. Maybe he discovers new jutsus that are unique to the monster world in school.
Perhaps some students who are jealous of Harry's fame could be antagonists. They might try to undermine him during training exercises.
It could be some powerful demon lords in hell. They might see Naruto as an intruder and try to stop him from whatever his goal is.
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.
The Akatsuki could still be the main antagonists. They might be interested in Naruto's tails for their own dark purposes, like using their power to create a super - weapon or gain control over the ninja world. Another option could be a secret group of rogue ninjas who have a vendetta against the Uzumaki clan and see Naruto's tails as a symbol of their power that they want to destroy.
One potential antagonist could be a new and mysterious organization that is similar to Akatsuki but with different motives. They might be interested in using Daisuke to open a portal to a different dimension or something like that. They would be constantly trying to kidnap Daisuke and force him to cooperate. Also, Orochimaru or his remaining followers could be antagonists. Even though Orochimaru has changed somewhat in the series, there could still be some of his followers who are more radical and want to use Daisuke for their dark experiments, believing that he has some special chakra or ability that could help them achieve their twisted goals.