JP was your average nineteen-year-old Trainer: he traveled, meeting new Pokémon and friends along the way, he battled, and he tried to earn badges. And, of course, he saved Pokémon from abusive Trainers and Poachers regularly.
All of that changed when Arceus put his plan of taking the Pokémon to a new world into action.
Now, JP, along with his Pokémon team, are in Equestria.
That, in and of itself, isn't too bad.
However, JP woke up as a Pokémon.
Now that could be problematic.