It could be a detective who is hell - bent on capturing Ash. This detective might have a personal vendetta or just be really dedicated to bringing criminals to justice.
Another possibility is that the main antagonist could be an organization. For example, a secret government agency that has its own reasons for wanting Ash captured. They might see him as a threat to their plans or simply as a symbol of chaos that they need to eliminate.
Maybe it's a rival criminal who wants to use Ash's situation to his own advantage. He could be trying to frame Ash for more crimes to get the heat off himself or to gain some sort of power in the criminal underworld. So, this rival criminal would be constantly working against Ash.
It could be a jealous rival trainer who mocks Ash for wearing a dress and tries to use it as a way to undermine his confidence and stop him from competing in Pokemon battles.
It could also be Lila. In this au, she could be a master manipulator who uses her lies to create chaos among the heroes and the citizens. She teams up with other criminals and uses her charm to get away with various crimes while making Ladybug and Chat Noir look bad. She might even be able to get her hands on some sort of powerful weapon or item that gives her an edge over the heroes.
A powerful werewolf could be the main antagonist. In the fanfiction world, werewolves and vampires often have a tense relationship. If Bella's sister does something that angers the werewolves, like stealing from their territory or harming one of them accidentally while doing her criminal deeds, the werewolf pack leader could become the main antagonist, vowing revenge on the sister and by extension, Bella and the Cullens.
Maybe a mysterious organization that wants to experiment on Latios. They believe that Latios holds the key to some sort of genetic or power - enhancing technology. They send out their agents, who are skilled in Pokémon capture and combat, to try and get Latios. They don't care about Ash at first, but when he stands in their way, they see him as an obstacle to be removed.
A powerful and greedy Team Rocket member could be the main antagonist. They might be after Diancie because of its rare and valuable powers. They could try to capture Diancie and use it for their own evil purposes, like selling its powers or using it to take over the Pokemon world.
Perhaps a dark - themed Pokémon organization that is researching the unique powers of Mudkip. They see Ash's Mudkip as a key to their experiments. So they send out their agents to capture it. These agents are skilled trainers with powerful Pokémon at their disposal, and they constantly pose a threat to Ash and his Mudkip throughout the fanfiction.
A powerful and greedy Pokémon collector could be the main antagonist. He wants to capture Ash, now in his Mew form, to add to his collection. He has all sorts of high - tech devices and trained Pokémon to try and catch Ash.
Maybe a powerful and envious Mewtwo could be the antagonist. Since Ash has now become a Mew, Mewtwo might feel threatened or think that Ash doesn't deserve such power. So, Mewtwo could try to fight Ash to prove his own superiority.
A wealthy and power - hungry trainer who wants to stop Ash from completing his Nuzlocke journey. This trainer believes that the Nuzlocke rules are too restrictive and wants to prove that his way of training Pokemon is superior.
A powerful and greedy Pokémon collector could be the main antagonist. He wants to capture all the rare Pokémon in Unova for his own collection, regardless of the consequences for the Pokémon or the ecosystem. He sees Ash and May as obstacles in his path, especially when they try to protect the Pokémon they encounter.