Story ideas

Mystery Dungeon
Have your main character turn into a pokemon and go on adventures, how he/she got there is up to you.

Make sure you give them a partner and include proper formatting.

Pokemorphs
Have your main character either be born with or gets the power to turn into pokemon. How the story runs is up to you.

Hybrid
Have your main character be kidnapped by a team of evil scientists and turn them into a pokemon/human hybrid.