I would very much like to see a water based dungeon in a n upcoming Zelda title similar to the Water Temple (OoT) or the Great Bay Temple (MM). I like both of those dungeons a lot, but the later Zelda games haven't had any water dungeons as grand as those specific two in my opinion. The last time we saw something that was at least something like them was the Lakebed Temple (TP), but that one did still not have quite the same feeling.
I don't know exactly what it is with those two water dungeons that makes me like them so much. It could be the atmosphere, but that might be difficult to recreate for an upcoming title, I don't know. Oh, and I'd like the boss to be somewhat similar to Morpheel (TP), but a lot harder.