I don't thin kthe Zelda games have particuarly good or original stores, btu I would make an exception in the case of
MM, which actually had more emotion in it, aswell as a darker theme. I don't think it's any coincidence that this game also forgoes the Zelda/Ganon/Link Triforce storylien that seems to be typical to most other Zelda games.
Seriously, out of all Nintendos's franchises, Zelda has the most potential for a decent storyline, which makes it a shame that there seems to be a lack of it in most of the games.