Ash could be one. He has a way of befriending all kinds of Pokémon, and his encounter with a friendly Mewtwo would be an exciting story. He could learn a lot from Mewtwo's psychic powers and wisdom.
Pikachu is also a likely main character. Pikachu's friendly nature could contrast with Mewtwo's initially aloof demeanor. They could have some really cute interactions, like Pikachu trying to cheer up Mewtwo when it's feeling down or Mewtwo using its powers to protect Pikachu from danger.
Brock could be a main character too. His knowledge of Pokémon care and his calm personality would be useful in a story with Mewtwo. He could be the one to first approach Mewtwo and start building a friendship, showing Mewtwo that humans can be trusted and kind.
Giovanni, the leader of Team Rocket, can be a very interesting character to include. His power - hungry nature and his past interactions with Mewtwo can add a layer of complexity to the story. There's also Misty. Her feisty personality and her skills as a water - type Pokemon trainer can bring a different dynamic to the fanfiction, especially if she teams up with Mew and Mewtwo or has some sort of rivalry with them.
Perhaps a new trainer who has a unique ability to communicate with Pokemon on a deeper level. This trainer, despite being new, has an innocent and pure heart. They see Mewtwo not as a monster but as a Pokemon in pain. So they step up to try and soothe Mewtwo's rage using their special gift.
In the 'pokemon mewtwo origin story', it was a group of scientists who created Mewtwo. They were trying to make a very powerful Pokemon by cloning Mew.
One interesting plot could be Mewtwo making friends with a group of Pokémon in a forest. They initially fear Mewtwo due to its power, but gradually come to understand its kind heart.
Obviously, the two Mewtwos are the main characters. They are the ones whose encounter drives the story forward.
The main characters are obviously Mewtwo, a powerful and genetically - engineered Pokémon, and Amber. However, there might also be other Pokémon characters that play important supporting roles, like Pikachu or Charizard, who could be friends or foes depending on the plot of the fanfiction.
There could be other Pokémon like Pikachu. Pikachu could be their friend who helps the little brother adjust to the new world. He could also offer some comic relief in the story. Another possible character could be Ash. Ash has a lot of experience with Pokémon, and he could offer some guidance to Mewtwo on how to take care of his little brother.
The main characters could be a Pokémon researcher and Mewtwo. The researcher is fascinated by Mewtwo's creation and wants to study it further. Mewtwo, at first, is suspicious but gradually warms up to the researcher as they spend more time together.
Maybe she gets separated from the other Mewtwos at a young age and is raised by a kind trainer. This trainer helps her to develop her powers in a different way compared to the other Mewtwos. Along the way, she has to face off against other powerful Pokemon who are jealous of her unique abilities and her relationship with her human trainer. As she grows, she becomes a symbol of hope for other female Pokemon who are often overlooked in battles and competitions.
Mewtwo is the main character. Also, Ash Ketchum and his friends are important characters. They are the trainers who are lured by Mewtwo to the island and get involved in the battles against Mewtwo and its clone Pokemon.