I liked the A Link to the Past model. In that game, some of the dungeons were themed, e.g. you had a desert dungeon, an ice dungeon, a water dungeon, and if I remember right a semi-lava-y dungeon (though I remember it as more of a fall-down-holes-a-lot dungeon, and the Link's Awakening version had most of the lava), but others weren't. They were basically just castles or temples or, you know, dungeons.
Also, in Link's Awakening, you had dungeons that may have been built around a theme, but it wasn't a standard elemental or climate theme. I'm thinking mainly of the Eagle's Tower: Now that was a creative dungeon. And, okay, "Tower" isn't much of a theme, per se, but it was something that could be made into something really cool. Then there was the Tail Cave, in which the theme was only visible in the map. (Unless I'm forgetting
I think the Zelda series needs to have a large stable of themes, rather than relying on the same few elemental themes over and over again. And the designers can't be afraid to come up with new themes. New variations on old themes are cool, too. (I wan't too fond of Twilight Princess's Goron Mines, but I applaud Nintendo for experimenting rather than rehashing OoT's Fire Temple or Dodongo's Cavern.)
Mixture of the old and the new is one of my favorite things about the Zelda series with regards to main gameplay gimmicks, so I don't see why it couldn't also apply to the dungeon designs.