After reading the text dumps, I don't necessarily believe Temple of Time or Temple of Hylia are anything more than plot-related buildings that you end up visiting. However, Sky Keep is surely a pretty large dungeon located in the sky. From the sounds of it, Sky Keep will be a typical final dungeon for Zelda: a final exam of all the things you learned to do in the game. There's one moment where Fi warns you that potions are necessary because there are no pots or chests that contain replenishing hearts.