Well, Epona is not really an actual character in the story of these new games. She was integral to the story of Ocarina of Time and Majora's Mask, but the new games are 10,000 years or more into the future, so Epona is long gone. Having her available through an amiibo is just a fun Easter egg, just like Wolf Link, Majora's Mask, the Biggoron Sword, or the Phantom Ganon armor. There are plenty of wild horses to tame which are actually part of this Hyrule and part of this story.