There have always been 2 Princesses of Equestria. In recent years, two more have joined the Royal Family. They rule with harmony and grace, and are loved by all Equestria. However, there once was a third with the two sisters. And HE still lives.
To protect his Pokemon from harm Arceus has moved most of his worlds populus to Equestria in hopes that they can live in peace, but peace is often harder to obtain than one might think.