One common theme is self - discovery. Since Mewtwo is a genetically - created Pokémon, a female Mewtwo in fanfic often has to figure out who she is and what her purpose is. Another theme is friendship. For example, she might make friends with other Pokémon or even humans.
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.
Rather than seeking 'lemon' (which often implies inappropriate content) fanfics, you could try to find fanfics that explore the unique abilities and personality of female Mewtwo in a more positive and creative way. For example, there might be fanfics where she teams up with other Pokémon to save the world or has an adventure in a new region.
A plotline might involve Ash as a female Mewtwo being hunted by some evil organization that wants to capture and study her. She then has to use her new form and wits to evade them. It could also include her trying to find a way to turn back into her original self while also learning about the secrets of the Mewtwo species.
Well, there's 'Female Mewtwo: Rebirth'. In this fanfic, the female Mewtwo has to face many challenges after being reborn in a strange new place. It's really interesting to see how she overcomes difficulties with her unique abilities. Also, 'Female Mewtwo's Friendship' is quite good. It shows how she forms special bonds with other Pokémon.
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.
A 'baby mewtwo fanfic' could be about the adventures of a young Mewtwo. It might explore its growth, its discovery of its powers, and how it interacts with the Pokémon world around it at a young age.
In an 'Ash into Mewtwo' fanfic, one aspect could be the change in relationships. His Pokémon might not recognize him at first, and he'd have to find a way to communicate and regain their trust. Also, trainers like Misty and Brock would be shocked. The fanfic could delve into how Ash tries to convince them that he's still the same person inside, just in a different form.
A 'pokemon mewtwo and missingno fanfic' could potentially tell a story where Mewtwo, the powerful and genetically - engineered Pokemon, crosses paths with Missingno, the infamous glitch Pokemon. It might be a story of how Mewtwo tries to understand or control Missingno, or perhaps they team up against a common enemy. There could be a lot of creative elements in such a fanfic, like new abilities for the Pokemon or a whole new world created just for them.
You can try searching on fanfic websites like FanFiction.net or Archive of Our Own. Just type in 'pokemon female mewtwo fanfic' in their search bars and you'll likely find some interesting stories.