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.
Another possibility is that there are ninja - like villains from the Naruto world who have also entered the Pokemon world. They might oppose Naruto because they have different goals regarding the Legendary Pokemon, like using them for their own selfish and destructive purposes back in the Naruto world.
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.
There could be a rogue legendary Pokemon that sees Ash's transformation as a threat to the natural order. This legendary Pokemon, with its own set of motives, could be trying to prevent Ash from becoming a fully - fledged legendary - like being. It might set up various obstacles and battles for Ash, testing his will and strength at every turn.
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.
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 group of dark - type Pokémon that have banded together and are trying to overthrow Arceus. They view Naruto as an easy target at first, but quickly realize he is a formidable opponent with his ninja skills and new Pokémon - related powers. They would constantly try to undermine Naruto and his efforts to protect the Pokémon world.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.
Maybe some corrupt officials within the prison system itself. They oppose Naruto's more humane and reform - focused approach to prison management. They might try to undermine him at every turn, for example, by cutting off resources or spreading false rumors about him among the prisoners.
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.
There could also be a trainer who is jealous of Harry's unique abilities, being reborn from the Harry Potter world. This trainer might try to undermine Harry at every turn, stealing his Pokemon or sabotaging his battles, much like Draco Malfoy was often in conflict with Harry in the original Harry Potter series.
Team Flare could be the main antagonists. They might see Baby Callum's connection with Pokemon as a threat to their plans in the XY region. Maybe they try to capture him or his Pokemon to stop him from interfering with their evil schemes.