The games are not right after each other. What I mean by this is that many of the games take place hundreds of games either before or after other games. Epona is not always the exact same horse in each game. The first time Epona was actually used was in OoT when Link finds her at Lon Lon Ranch. Then in MM, Link and Epona are the same from OoT and Link takes her with him in his new adventure. Epona was also introduced in the Oracle of Ages and Seasons games. You don't really use her, but you see her at the beginning of the game right before the title screen. TWW did not feature Epona because she wasn't needed due to the ocean. And Epona is in TP because Link is a horseman and lives in a small village where their major products are cattle and cheese. Link needed to be a master horseman because the village needed him to be.
So, Zelda games do not always need Epona in the game. She usually isn't needed and she wasn't even introduced into the series until after a lot of games were released. So, there really isn't a need to be concerned with where she is in games that she's not in. She's only a horse and if she's needed, she'll make an appearance.