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.
Perhaps some of the jealous monster students who don't want Naruto to succeed in school could be antagonists.
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 group of radical female ninjas who see Naruto as a threat to their new - found power structure. They may want to get rid of him to ensure that the world remains under their complete control.
There could be a demonic entity in the new world. It might be awakened by Gilgamesh's arrival. This entity is used to having its way in the world and sees Gilgamesh as a new obstacle. It could possess other beings to attack Gilgamesh and use the chaos of the new world to its advantage.
It could be an evil version of Sasuke. In the original story, Sasuke had his dark moments, and in a very dark fanfic, he could be fully consumed by evil and oppose Naruto in a much more malevolent way.
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.
In a magical world, a powerful sorcerer could be the antagonist. This sorcerer views Tony's attempts to blend technology and magic as an abomination and will do everything in his power to stop Tony from spreading his ideas and inventions. He might even try to steal Tony's technology for his own dark magic purposes.
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.