>Pokémon Legends Mewtwo, set in an old Kanto where you get in contact with a newly born Mewtwo and have it as your companion for the whole game.
>As the game progresses Mewtwo gets more and more abilities and in the end it'll unlock his whole potential to the point he'll be able to fly.
Mewtwo near the end of the story gets exploited by evil scientists into be used for experiments and the player dies saving it, but Mewtwo saves him/her by extracting the player conscience and bringing it in its head.
>In the end Mewtwo will be fully controllable thanks to the player coexisting in its body and using all its abilities.
>At one point Mewtwo becomes unstable because 2 conscience in one body is too much for the capability it has at the time, to the point that the player sacrifices himself and asks Mewtwo to not be alone and that's when Mewtwo goes to Cerulean Cave in pain and then meets Red, following his old friend's advice

I want Game Freak to make a story like this