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.
One idea could be that Ash gets transported into the FNAF world while on a Pokemon journey. He might use his Pokemon's abilities to survive the creepy animatronics. For example, Pikachu's electricity could short - circuit some of the malfunctioning animatronics.
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.
Obviously, Ash is one of the main characters. Since it's about him being a legendary Pokemon in this fanfiction, he's central to the story.
Since it's an 'ash the pokemon fanfiction', Ash is the central figure. But it could also feature his friends from the original series like Misty and Brock. And of course, the villains he encounters would be important characters too. There may be new characters created by the fanfiction writer, such as a mysterious trainer who has a rare and powerful Pokemon that Ash has to face.
Pikachu is a very likely candidate. It's Ash's most iconic Pokemon and has a deep bond with him. Whenever Ash is in trouble, Pikachu often steps up to protect him.
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.
Ash is obviously one of the main characters. He is at the center of the harem concept. Then there would likely be a group of human characters who are part of his harem, though their specific identities can vary greatly depending on the fanfiction.
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.
Obviously, Ash is one of the main characters. He's the protagonist who has a passion for pokemon and is always eager to become a pokemon master. And the legendary pokemon he encounters or befriends would also be important characters. For instance, if it's Lugia, Lugia would play a major role in the story as it's a very powerful and mysterious pokemon.
Another common theme is transformation. There are fanfictions where FNAF characters are transformed into Pokemon or vice versa. This allows for exploring new abilities and relationships. Also, survival is a theme. Just like in FNAF, the characters in the fanfiction might have to survive in a strange new world that combines the two universes, using the skills from both Pokemon and FNAF.