There could be a rogue legendary Pokemon that sees Ash's transformation as a threat to the natural order. This legendary Pokemon, with its own set of motives, could be trying to prevent Ash from becoming a fully - fledged legendary - like being. It might set up various obstacles and battles for Ash, testing his will and strength at every turn.
Maybe Ash discovers a hidden power within himself that is linked to the legendary Pokemon. This power could be awakened through a series of dangerous adventures, like facing off against an evil team that is trying to capture all the legendaries. As he progresses, he gradually transforms into a being with some of the abilities of a legendary Pokemon.
Articuno, Zapdos, and Moltres are quite common. Their elemental powers and the mystery surrounding them make for great fanfiction material. Ash might encounter them during his travels and have to either help them or face off against them in some way.
One of the Legendary Pokemon could be Giratina. Despite its somewhat dark and otherworldly nature, Giratina might be intrigued by Ash's light - heartedness and his ability to make friends with all kinds of Pokemon. Dialga and Palkia could also be part of the harem. Dialga, with its control over time, might see Ash as an important factor in the future of the Pokemon world. Palkia, in charge of space, could be interested in how Ash navigates different regions and spaces in his journey. And don't forget about Ho - Oh. Ho - Oh is a symbol of hope and might see Ash as a bringer of hope in the Pokemon world, thus joining his harem.
Arceus is quite popular. Given that it's considered the creator of the Pokemon universe in the official lore, it often has a significant role in fanfictions. Mewtwo is also very common. Its powerful psychic abilities and complex backstory make it a favorite for fanfic writers to explore. Another popular one is Lugia. With its majestic appearance and its connection to the sea, it's often a central figure in many stories.
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.
It could be Team Rocket - style villains who want to capture Naruto because they think he has some special power that can help them control Legendary Pokemon. They might try to trick him or set traps for him.
One possible main antagonist could be a powerful and arrogant trainer who wants to prove that he is better than Ash and Nora. He might try to steal their Pokemon or sabotage their battles.
The appeal lies in seeing Ash in new and exciting situations. With legendaries involved, his journey becomes more epic. It's like taking the underdog story of Ash in the anime and supercharging it.
In Ash-centered legendary Pokemon fanfiction, often Ash has extraordinary adventures. He might form unique bonds with legendary Pokemon that are not seen in the official storylines. For example, he could befriend a Mewtwo and together they face off against an evil organization trying to clone more powerful Pokemon. These fanfictions allow for a lot of creativity, expanding on Ash's character and his relationships in the Pokemon world.
One possible antagonist could be Orochimaru. He might be interested in Naruto's new Shadowman powers and try to steal them for his own evil purposes.