Red could be a great main character. He's one of the most iconic Pokemon trainers. You could tell the story of his journey from a different perspective, like how he got his first Pokemon and what his real motivations were at the start of his adventure.
A mysterious and unknown trainer who discovers a new and powerful Pokemon species could be the main character. This trainer then has to protect this new species from those who would misuse it while also trying to understand its origin and place in the Pokemon world.
There might be some legendary Pokemon that are guardians of the Hall of Origin. For instance, Arceus could be a key character, as it has a strong connection to the Hall of Origin. And then there could be other trainers who are either rivals or allies of the main trainer in the story. They could all have different motives regarding Necrozma and the Hall of Origin. Some might want to capture Necrozma for its power, while others want to protect it or the Hall of Origin from harm.
A student who is not from a traditional Pokemon - training family but has a natural talent for understanding Pokemon behavior. They face some discrimination from other students at first but gradually prove themselves. Their main Pokemon could be a Bulbasaur that they've had since they were a child, and together they navigate the complex social and academic environment of Pokemon University.
There's Dawn, who is very passionate about her Pokemon training. Also, Lillie from the Alola region, with her kind and gentle nature. Bianca, with her ditzy but endearing personality, could be an interesting addition to the harem in a Pokemon Games fanfic.
Twilight Sparkle from My Little Pony could be a main character. She's very intelligent and curious, so she'd be interested in learning about Pokémon. Ash from Pokémon could also be a main character as he's always up for new adventures and meeting new creatures. Together, they could lead the story, with Twilight using her magic and Ash his Pokémon - training skills.
Obviously, Melmetal could be one of the main characters. Another could be a trainer with a special connection to Melmetal.
An older trainer who has retired from the Pokemon circuit but is pulled back into action by a mysterious event related to a strange Pokemon. This character would have a wealth of knowledge and experience that they can draw upon during their new journey. They might also have some old rivalries that resurface during the story. Another potential main character could be a Pokemon itself. Maybe a Pikachu that has unique abilities and decides to embark on its own journey to find out more about its powers and where it came from.
A young Pokemon researcher could be a great main character. They're eager to learn about the unique Pokemon in Hoenn and end up getting involved in all sorts of adventures while studying them.
An old - fashioned Pokemon breeder who has a deep connection with the traditional ways of raising Pokemon. They could provide the main characters with valuable advice on how to make their Pokemon stronger and healthier. However, they might also be a bit stubborn about sticking to the old ways and this could cause some conflicts with the more modern - thinking characters in the fanfic.
Obviously Naruto would be the main character since it's about him being reborn as a Pokemon fan. His Pokemon partners could also be considered main characters. For example, a Pikachu that he befriends early on and they go on adventures together.
A young and ambitious sand ninja named Kaito could be a great main character. He's eager to prove himself and rise through the ranks in Sunagakure. Another could be a female ninja, Saya, who has a special jutsu related to sand manipulation that sets her apart. Or perhaps an older, more experienced ninja, Ryuji, who has seen many battles and has a lot of wisdom to offer but is also haunted by his past actions in the service of the village.