It could be a scientist who is involved in the study of Pokemon genetics. While trying to understand the mechanics of evolution better, they accidentally stumble upon the new evolution and then become involved in the events that unfold as a result, both in the scientific and the trainer communities.
It could also revolve around a genetic experiment gone wrong that accidentally creates a new form of evolution for some Pokemon. These newly evolved Pokemon are initially feared but eventually prove to be helpful in a crisis situation, teaching the humans and other Pokemon the importance of acceptance and adaptability.
It could be a young and inexperienced trainer who is just starting their journey in this new world. They have big dreams but a lot to learn.
It could be a Pokemon itself. For example, a Pikachu that has been separated from its original trainer and has to fend for itself in the wild. But then it meets a new friend, either a human or another Pokemon, who helps it start over. This Pikachu could be the focus of the story as it overcomes its past traumas and looks forward to a new life.
Obviously, the main character could be the new Magma Grunt. He could be a fresh recruit with a different perspective compared to the more experienced members of the team.
It could also be an experienced pokemon trainer who has seen a lot in their travels. After encountering a mirage pokemon by accident and realizing how different and powerful they are, they become determined to become the mastermind in the world of mirage pokemon. They use their existing pokemon training skills and knowledge to study these special pokemon, making them a formidable force in the fanfiction.
A Ditto could be the main character. Since it can transform into other Pokemon, it could have a unique perspective on different Pokemon species and their lives.
Squirtle. Squirtle is cute and friendly. If it adopted a human child, it could show the child the underwater world of Pokemon. The Squirtle could teach the child how to swim, and they could explore underwater caves together. It would be a really fun and light - hearted story with Squirtle as the main Pokemon.
A Charizard might be the main character. Imagine a Charizard that was always too proud and aggressive. Then it turns over a new leaf and becomes more gentle and uses its fire - breathing ability to help others, like warming up cold areas or helping with cooking in a village.
The main character could be a talented pokemon stylist. They have a passion for making pokemon look their best with unique haircuts. They travel around different regions to learn new haircut techniques and to show off their skills on various pokemon.
It could be Ash. He's the classic Pokemon protagonist and has been through so many trials already. His will has been tested countless times, like when he faced the Elite Four or when he had to rescue his Pokemon from Team Rocket. In this fanfiction, he could face a new kind of test that really pushes his will to the limit.