It could be a jealous trainer. This trainer might see Ash in his shiny pokemon form and want that power for himself. So he tries to capture Ash by any means necessary, setting up all kinds of traps and challenges for Ash and his friends.
Maybe a group of evil scientists. They are interested in Ash's transformation and want to study him. They don't care about Ash's feelings or well - being and will stop at nothing to get their hands on him. They could use all kinds of high - tech devices to try and capture him, which would put Ash in a really tough situation.
There could be a powerful shiny pokemon that sees Ash as an intruder in the shiny pokemon world. This shiny pokemon is very territorial and doesn't like the idea of a human - turned - shiny - pokemon in its territory. So it constantly attacks Ash and tries to drive him out, making it a major obstacle for Ash to overcome in the fanfiction.
There could be a new, evil organization in the fanfiction. Their goal is to use shiny pokemon to power some sort of dark machine or experiment. They target Ash's shiny pokemon because it has a particularly strong energy. This organization would send out their minions to attack Ash and try to capture the shiny pokemon, creating a lot of action - packed scenes in the story.
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 jealous male trainer could be the main antagonist. He might see Ash's transformation as an unfair advantage given by some mysterious power. He constantly tries to undermine her in battles and challenges, believing that a female should not be as successful as a male in the Pokemon world.
Well, perhaps Ash could gain new and amazing powers. Shiny pokemon often have special abilities or appearances, so if Ash turns into one, he might be able to fly like a shiny bird - type pokemon or have super strength like a shiny fighting - type. He could also use his new form to communicate better with pokemon, since he'd be more like them.
Team Rocket could still be the main antagonists. They might see Ash as a Pikachu and try to capture him more than ever, thinking he's a special Pikachu. Maybe they believe he has some sort of new power because of his transformation.
Maybe Team Rocket could be the main antagonist. They might see Ash's transformation as an opportunity to finally capture Pikachu. Since Ash is in a more vulnerable state as a girl, they could try to use different tactics to take advantage of the situation.
Perhaps a jealous trainer. This trainer has always been envious of Ash's success and now that Ash is in a vulnerable state as a Zorua, the trainer sees an opportunity to get rid of him for good. The trainer could try to use his own Pokémon to capture Ash or even harm him, making the trainer a formidable antagonist in the story.
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.
Perhaps a dark - type Pokémon that is jealous of Ash's new form. This Pokémon might see Ash as a threat and constantly try to attack him and stop him from getting used to his Latios form.
It could be a Team Rocket member who has obtained a new device. This device was meant to transform Pokemon into other forms for their evil purposes. But by accident, it affects Ash instead. So, this Team Rocket member becomes the main antagonist as he tries to either capture Ash in his new Glaceon form or use him for other devious plans.