"With each person, you get up to three Pokémon within each specific area, with the third Pokémon slot appearing should the person have defeated the Elite Four, with them getting Hidden Abilities if the player has been online at the same time as you. It also appears that the Pokémon found within the Friend Safari have got two IVs of 31."
Maybe we need to be in the game together to get my third slot? I should have three; I defeated the Elite 4.