An external force like a neighboring underwater empire might send spies or agents to disrupt Harry's rule. These could be the antagonists as they try to create chaos in Atlantis to make it easier for their own empire to take over.
A powerful sorcerer or wizard from within Atlantis who has his own designs on the throne could be an antagonist. This character might see Harry as an obstacle to his own power - hungry plans.
One possible main antagonist could be an Atlantean sorcerer who is jealous of Harry's growing influence and power in Atlantis. This sorcerer might have his own plans to rule Atlantis and sees Harry as a threat. Another could be a group of traditionalist Atlanteans who oppose any foreign influence, like Harry's, and they try to undermine his attempts to bring new ideas and magic from Hogwarts.
The Titans could still be a major threat. Even though they were mostly defeated in the original series, some of their followers might see Percy's new role in Atlantis as a threat to their plans for chaos. They could try to undermine Percy's position in Atlantis and use the underwater city as a base for a new uprising.
Voldemort and his Death Eaters could still be the main antagonists. Since Harry is now seen as a prince, they might see him as an even greater threat to their dark plans and try to eliminate him.
Obviously, Harry Potter would be one of the main characters. And there would probably be some Atlantian characters like the King or Queen of Atlantis, or other important Atlantian figures. Maybe some of Harry's friends from Hogwarts could also be involved, like Hermione and Ron, if they also get dragged into the Atlantis adventure.
One possible storyline could be Harry's journey in learning the complex politics of Atlantis as the crown prince. He might face challenges from rival factions within the underwater kingdom.
The Ministry of Magic could be the antagonists. Since Harry is in a gang, they might see him as a threat to the order of the wizarding world. They could send Aurors after him and his gang mates, trying to arrest them and break up the gang.
The Titans could be the main antagonists. They might see Naruto as a threat to their plans of regaining power in Olympus. Since Naruto is trying to uphold the order in Olympus, the Titans would oppose him.
Some of the teachers at U.A. might also be antagonists. They could be secretly working for an organization that wants to control Izuku's powers for their own evil purposes. They would pretend to be helpful while actually setting traps and spreading misinformation about him.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.
Some of the more traditional pure - blood families in the wizarding world could be antagonists. They might not approve of Harry, a half - blood, being involved with Pansy, and they could try to stop the pregnancy or break up the couple for the sake of 'pure - blood' ideals.