A young and determined trainer named Kai could be a main character. He has a Pikachu that he has trained to use ninja - like moves, such as lightning - fast dodges. Kai is always eager to take on new challenges and prove himself as a great pokemon ninja trainer.
There could be a female character, Ayumi. She comes from a long line of pokemon ninja trainers. Her main pokemon is a Eevee that she has taught to transform into different forms for different ninja - like functions. Ayumi is very strategic and often uses her wits more than brute force in battles.
One idea could be a group of pokemon ninja trainers who have to protect a rare and powerful pokemon from an evil organization. The trainers could use their ninja skills, like stealth and quick attacks, along with their pokemon's abilities to outwit the villains.
Often, the main characters are still the trainers and their pokemon, but with their roles switched. So the pokemon that were secondary characters in the original concept become the ones driving the story. For example, Pikachu could be the main character leading Ash around instead of the other way.
Obviously, Ash is one of the main characters. He is usually at the center of the story, using his skills as both a Pokemon trainer and a ninja. Pikachu is also a very important character, often using its electric powers in combination with Ash's ninja - like strategies. Sometimes, other trainers like Brock and Misty can also be important characters, providing support or joining in on Ash's ninja - themed adventures.
Hermione Granger could also be a main character. With her intelligence, she would be quick to learn ninja techniques and could even help improve them with her knowledge of magic. She might study the ancient ninja scrolls and find ways to combine the knowledge of both worlds for the greater good.
The main character could be a young trainer named Ash. He's always eager to learn more about Pokemon and is very friendly. Another character could be Misty, a girl who is really good with water - type Pokemon and is a bit of a tomboy. There could also be Brock, who is knowledgeable about Pokemon care and often gives advice to other students.
The Kratt brothers, Chris and Martin, would definitely be the main characters. They could bring their knowledge of animals from 'Wild Kratts' into the Pokemon world. Their Creature Power Suits could be modified to work with Pokemon in some way. And of course, their sidekick, Aviva, could also be a main character, helping them create new devices to interact with Pokemon.
It could be Ash as Romeo and Misty as Juliet. Ash is always on adventures and Misty has her own goals. Their different approaches to Pokemon training could be like the differences between the families in Romeo and Juliet. And they could have a budding romance that is complicated by their own goals and the Pokemon world around them.
One main character could be a human scientist who was once respected by the Pokemon for their knowledge but is now enslaved. They use their scientific skills to try and find a way to free themselves and others. On the Pokemon side, there could be a young and curious Pokemon that starts to question the practice of enslaving humans and eventually becomes an ally to the humans. And of course, there could be a powerful and mysterious Pokemon that is the mastermind behind the entire enslavement operation.
A young and inexperienced trainer who discovers they have latent psychic abilities and uses them to bond with their psychic Pokemon. This character could grow throughout the story as they learn more about their powers.
The main characters could be the Fire and Ice Pokemon themselves. For example, a Flareon and a Glaceon. They could be on a quest to find a special crystal that can balance the power of fire and ice in their world. Their interactions and growth throughout the journey would be the focus of the fanfic.