Spoilers, the starters are a ruse. You start play as a successful gym leader, but you get your teeth kicked in and your pokemon taken by the villainous team at the very start, and get left for dead in the wilderness with one pokeball. You get a cutscene in which you capture a rattata, and have to fight your way back to civilization, and start the arduous path back to power and to defeat the team that has successfully taken over the world.
The starter you pick eventually becomes a rare captureable wild pokemon.
