The obvious villains could be the malfunctioning animatronics from FNAF. They could be acting under some sort of dark influence and see Ash and his Pokemon as intruders to be eliminated.
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.
A new, mysterious group of poachers could be the villains. They might be after rare and powerful Pokemon to sell them on the black market. These poachers could be highly organized and have advanced technology to capture and keep the Pokemon hidden. Another option could be a lone, power - hungry trainer who believes that by kidnapping the strongest Pokemon, they can become the ultimate Pokemon master. They might not care about the well - being of the Pokemon, only seeing them as tools to achieve their own goals.
Maybe Team Rocket could have a new member who is a ninja. This new member could be Ash's main rival. They would try to steal Ash's pokemon in more sneaky and ninja - like ways. And Ash would have to use his ninja skills to protect his pokemon and defeat this new rival from Team Rocket.
There could be a new, unknown group of villains in the fanfiction. They might be after a special type of Pokemon that is native to Unova. These villains could be using underhanded tactics to catch these Pokemon, and Ash and May would have to uncover their motives and stop them. For instance, they could be trying to use the power of these Pokemon for their own selfish gains, like taking over Unova's Pokemon centers or disrupting the Pokemon league.
A new villain could be a powerful and dark psychic - type Pokemon. This Pokemon could have the ability to turn Ash into a Pokemon as part of its grand plan to take over the Pokemon world. It sees Ash, who has always been a symbol of hope and a strong trainer, as a threat even in his human form. So, by turning him into a Pokemon, it hopes to disrupt the balance and order that Ash has been a part of maintaining.
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.
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.
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.
It could be a jealous rival trainer. This trainer might have always been envious of Ash's popularity and the loyalty of his harem. So, they plot and scheme to turn the harem against Ash by spreading lies and creating discord among them.