Well actually, your hero and Hideyoshi can transform two times. To get to level 3, you must complete all side quests, or 16 senior quests, finishing with nobunga, to get the hero quest, you then must have eevee, or any of it's evolutions to 80% or higher, you then transform after that battle, and arceus appears. So don't worry if you have 6 linked pokemon already. Hideyoshi on the other hand, you have to get infernape to 65%, then have Reshiram to 70%, to get him to his last trasnformation. Other then that, all the others only transform once.