Another possible antagonist could be a rogue Titan from the Titan world who somehow makes its way into the Naruto universe. This Titan could be enraged or corrupted and see Naruto as an enemy because of his mixed heritage. It could cause destruction across the ninja world, and Naruto would have to stop it using his ninja skills and Titan powers.
It could be Orochimaru. Since Orochimaru is always after powerful ninja and their abilities, if Naruto is now the son of Asuma, he might see Naruto as a new target with unique potential.
One possible antagonist could be those who oppose the mixing of the Naruto world and the Greek mythology elements. They might see Naruto as an abomination because of his unique heritage as the son of Demeter. Another could be some of the traditional Naruto villains who now see Naruto as an even greater threat due to his newfound powers related to Demeter. For example, Orochimaru might be interested in Naruto's powers for his own evil experiments.
One possible main antagonist could be a rogue ninja who was once an apprentice of Orochimaru and is jealous of Naruto's connection to the Sannin. This ninja might want to steal Naruto's new - found powers related to the Sannin. Another could be a hidden organization that sees Naruto as a threat because of his potential with the Sannin's abilities. They fear he will disrupt their plans for power in the ninja world.
One possible antagonist could be a jealous Roman god who doesn't want Naruto, as the son of Jupiter, to gain too much power. Maybe Pluto, who might see Naruto as a threat to his own domain in the afterlife.
The Akatsuki could still be major antagonists. Their goals of collecting the tailed beasts would put them in direct conflict with Naruto, especially if he has the added power from his relation to Esdeath. They might see him as an even greater threat.
It could be some of the traditionalist ninjas in the Mist Village who oppose Naruto because of his status as the Mizukage's son. They might see him as a threat to their old - fashioned ways.
The Akatsuki could still be the main antagonists. Even though Naruto is the'son of god', they might see his power as a threat to their own goals. For example, Pain might believe that Naruto's new - found status will disrupt the cycle of pain and suffering that he wants to maintain in the world.
One main antagonist could be Lex Luthor's business rivals from his world. They might see Naruto as a way to get to Lex Luthor, so they would constantly try to capture or harm him. Another could be some of the traditional Naruto villains who sense this new threat in the form of Naruto with his unique heritage and abilities. They would want to eliminate him before he becomes too powerful.
In the RWBY world, Salem could be a major antagonist. She might view Naruto's son as a threat to her plans for Remnant. His unique powers and knowledge from the ninja world could potentially disrupt her schemes, so she would try to eliminate him.
There might be a group of tomb raiders who are jealous of Naruto's connection to Lara Croft. They see him as an obstacle in their path to obtaining great treasures. Also, some dark forces from both universes could team up. For example, Orochimaru from the Naruto world might make a deal with a villain from the Tomb Raider world to get access to Naruto and his unique powers for their own evil experiments.