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.
An evil ninja from Naruto's world who has also found a way into the Pokemon world. This ninja could be jealous of Naruto's newfound friends and power in the Pokemon world. He decides to team up with some of the criminal elements in the Pokemon world to try and take down Naruto and rule over both worlds.
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.
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.
It could be a rogue ninja who also has strong water - based abilities and wants to prove that he is the true master of water. He might see Naruto's newfound skills as a threat.
A rogue ninja who has mastered all the dark aspects of the elements could be a great antagonist. This ninja could use their powers to create disasters, like summoning tsunamis with water element or causing volcanic eruptions with fire element. They might have a vendetta against the Hidden Leaf Village and see Naruto as a threat to their plans because of his growing elemental powers.
It could be a rogue ninja who also has some form of magnetism - based power but uses it for evil. This ninja might be jealous of Naruto's natural talent and wants to prove that he is the stronger one.
It could be a rogue ninja who also has mastered Nen. He might be jealous of Naruto's newfound power and wants to steal it for himself.
Perhaps an ancient demon that was once sealed away but has now been released due to some unforeseen circumstances. The demon has an affinity for fire and sees the Fire Master as a threat to its plans of world domination. It would constantly try to eliminate the Fire Master and anyone who stands in its way, including Naruto and his friends.
Perhaps an ancient evil spirit that was sealed away long ago and is now awakened by the power of Spinjitzu. This spirit wants to use Spinjitzu to destroy the ninja world, and Naruto has to stop it.
It could be a rogue ninja from a hidden village who has also mastered lightning jutsu and wants to prove himself stronger than Naruto. This ninja might have a personal vendetta against Naruto or Konoha.