A jealous rival from the main character's hometown could be the antagonist. This person has always been in the main character's shadow and is now determined to ruin their journey to become a Pokemon master. They might use underhanded tactics like spreading false rumors about the main character or sabotaging their Pokemon during battles.
Perhaps an organization that believes in using Pokemon for cruel and unethical experiments. They view Pokemon as mere tools and are trying to create super - powerful Pokemon through these experiments. They see the main character, who has a more harmonious relationship with Pokemon, as a threat to their plans.
It could be a former ally of the Pokemon Master who has turned evil. Maybe they felt overshadowed by the Pokemon Master and now seek revenge. For example, they might have found a dark artifact that corrupts them and gives them the power to control other trainers' Pokemon.
Team Rocket from the Pokemon world could be the main antagonist. They might see Naruto as a threat to their plans of stealing powerful Pokemon. They could try to use their usual sneaky tactics on Naruto, but he would be too smart for them with his ninja training.
A young and determined trainer named Alex could be the main character. Alex has grown up in a family of Pokemon trainers but wants to make a name for themselves in a unique way, not just following the family's footsteps. They set out on the road to master with a starter Pokemon that has some unusual traits.
Maybe a new villain organization that believes in a different way of training Pokemon, a cruel and unethical way. They see Ash as a threat to their ideology because he is a symbol of the traditional, kind - hearted Pokemon training. So they constantly try to stop him from achieving his goal of becoming a Pokemon master. For example, they might try to steal his Pokemon or sabotage his battles.
I don't know for sure as I haven't read it. It could be a new trainer starting out on their journey to become a master.
It could be Voldemort who somehow follows Harry into the Pokemon world. He might try to use the power of Pokemon to regain his strength and take over both the wizarding world and the Pokemon world. His dark magic could corrupt some of the Pokemon, turning them into his minions.
It could be a group of Team Rocket - like villains. They are after the unique powers that the reborn pokemon might possess. Since the reborn pokemon has a human - like intelligence, they see it as a valuable asset to use for their evil plans, like stealing all the precious pokemon resources or taking over a certain region.
It could be a powerful and evil Pokemon trainer who wants to capture Ash in his new Pokemon form. This trainer might be after Ash because he believes that a human - turned - Pokemon has some special power or value.
Maybe a powerful and evil pokemon trainer who has a vendetta against Ash. Now that Ash is in a vulnerable pokemon form, this trainer could try to capture and control him. The trainer might have some dark motives related to using Ash's unique situation to gain power in the pokemon world.
The main character in this fanfic is probably a trainer who is eager to master Pokémon training. Alongside them, there could be a group of friends who are also trainers at different levels of their own journeys. There might be a Pokémon that has a special bond with the main character, perhaps a Pokémon they've had since they were very young. And then there could be a mysterious character who appears from time to time, with knowledge about rare Pokémon or secret training techniques that help the main character on their road to mastery.