There could be other rogue ninja groups who see Naruto's sister as a threat or a valuable asset. They might try to either eliminate her or force her to join them. These groups would be antagonists as they oppose her in her new rogue lifestyle and she has to constantly fight or outwit them.
One possible plot could be that Naruto's sister feels overshadowed by Naruto's achievements in the village. She might start to question the village's values and leadership. As a result, she gradually becomes a rogue, believing she can find her own path outside the constraints of the village. Maybe she teams up with some outcasts who also have grudges against the village.
The Akatsuki could be the main antagonists. Since Naruto is an important target for them, and if Kurenai is now his sister, they might see her as an obstacle in their way. They could try to use their various powers and strategies to either capture Naruto or cause harm to both him and Kurenai.
The main antagonists could be the traditional Naruto villains like Orochimaru or the Akatsuki members. They might target Naruto's sister as a way to get to Naruto, seeing her as a weakness or a way to manipulate him.
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.
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.