Another antagonist could be a powerful and corrupted legendary Pokemon. It could be causing chaos in the Pokemon world and Naruto would have to use his skills and the power of his Pokemon team to stop it. This would be a great challenge as legendary Pokemon are extremely powerful, but Naruto has his own set of unique abilities that could give him an edge.
It could be Team Rocket - style villains who want to capture Naruto because they think he has some special power that can help them control Legendary Pokemon. They might try to trick him or set traps for him.
It could be dark ninjas who oppose Naruto's new role as the God of Nature. They might want to use the power of nature for their own evil purposes, like creating disasters to gain control over regions.
Another possibility is that the very entity that bestowed god - like powers on Naruto has an ulterior motive. It could turn out to be the true antagonist, using Naruto as a pawn in its grand scheme. This entity might be manipulating Naruto to cause chaos in the ninja world so that it can feed on the negative energy or fulfill some other dark purpose.
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.
Perhaps an evil Pokemon scientist who has created a device that can control the minds of Pokemon. He discovers Naruto's arrival and sees him as a threat. So, he teams up with some of the most powerful and aggressive Pokemon to stop Naruto. He has no regard for the well - being of Pokemon or the balance of the world, only his own ambition to rule.
It could be a new group of ninjas who oppose Naruto's new - found power as the 'god of blades'. They might be jealous or see him as a threat to their own power - hungry plans.
It could be Team Rocket. They are always after rare and powerful Pokemon, and a female Nine - Tails Pokemon would be a prime target for them. They might try to capture her using their devious schemes and mechanical contraptions.
It could be other shinobi who envy Naruto's new - found connection to the primordial god. They might see his power as a threat to their own status and ambitions, and thus try to undermine or even kill him.
Perhaps a powerful and mysterious trainer. This trainer is jealous of Ash's connection with his Pokemon and his ability to conduct these experiments. He wants to prove that he is the better trainer. So he tries to disrupt Ash's experiments by challenging him to battles at inconvenient times. He also spreads false rumors about Ash's experiments being dangerous to other Pokemon, which causes some local Pokemon communities to be hostile towards Ash.
Maybe a powerful and corrupted Pokemon that has gained sentience and wants to rule both the Pokemon world and Naruto's world. It sees Naruto as an obstacle because of his godlike powers. This Pokemon could have the ability to control other Pokemon and use them to attack Naruto and those who oppose it. It would be a major antagonist as Naruto has to find a way to defeat it and restore peace to both worlds.