It could be a young and ambitious wizard. Wizards often have the power and knowledge to take over a world in fantasy stories.
Perhaps a scientist who has been studying Pokemon for years. When Pokemon start to rule the world, this scientist uses their knowledge to figure out how to live in this new situation. They might try to find a way to reverse the situation, or at least make sure that humans are treated fairly under Pokemon rule.
One main character could be a civilian engineer who devises new technologies that make the civilians less dependent on the ninja for protection. Naruto would be involved as he is always in the middle of any major change in the Naruto world. Additionally, a civilian diplomat who is able to negotiate with different ninja clans and villages on behalf of the civilians could be a main character. This diplomat would play a crucial role in getting the ninja to accept the idea of civilian rule.
It could be a new Uchiha character created specifically for the fanfic. This character could be an outcast Uchiha who has been living in hiding, observing the village's problems from afar. He decides to come back and use his unique Uchiha abilities, combined with a new perspective on life, to rule the village and bring about change. He would be an unknown force that disrupts the status quo.
Well, it could be about a character who discovers a new world and through various adventures and challenges, gradually gains the power to rule it. Maybe they start as an underdog and have to learn the ways of this new world, make allies and defeat enemies along the way.
The plot could involve Pokemon taking over all major industries. For example, they could run the power plants using their unique abilities like Electric - type Pokemon generating electricity. People would have to rely on Pokemon for transportation too, with Flying - type Pokemon as aerial taxis.
One possible plot could be that civilians in the Naruto world get tired of being overshadowed by the ninja clans. They start a peaceful revolution, using their knowledge and skills in non - combat areas like trade and diplomacy. Naruto, being a ninja who has always valued the common people, could support their cause secretly, leading to a new world order where civilians have a more equal say in governance.
It could be an ordinary person from our world, like a high - school student. They would bring their own set of values and knowledge from the real world into the pokemon world. This contrast between the two worlds could create a lot of interesting storylines.
Since I haven't read it, I can't say for sure who the main characters are.
A young girl who has always dreamed of the Harry Potter world could be the main character. She could be transferred there and discover she has some latent magical abilities that are unique even in the wizarding world.
A descendant of one of the original founders of Hogwarts. They might have some special connection or mission related to the school and the wider wizarding world. They would travel around to uncover secrets about their family's past and the history of the magical places.