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.
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.
In an 'Ash turns into Latios' fanfiction, perhaps Ash is turned into Latios as a way to better understand the Pokémon he has befriended. As Latios, he might be able to communicate with other Pokémon on a deeper level. For example, he could learn the secrets of legendary Pokémon that have always been a mystery. His friends, like Pikachu and Misty, would initially be shocked but then have to figure out how to help him reverse the transformation or support him in this new form.
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.
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.
The plot could start with Ash stumbling upon an ancient artifact or a cursed place. As he touches or enters it, he is suddenly transformed into Latios. At first, he struggles to control his new form and powers. He might accidentally cause some chaos in the Pokémon world. His friends then set out to find a way to turn him back. Along the way, they encounter various obstacles and meet other Pokémon who either help or hinder their quest.
Maybe Ash gets magically transformed into a Latios. He then discovers he can fly and uses his new powers to explore regions he couldn't reach before as a human. He might also meet other Pokémon in a different way and form new friendships.
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 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.