Axle had a good point in his recent
article that "dark" really depends on a person's definition. His example was the dread and anxiety in Majora's Mask, versus the themes of sadness and loss in Twilight Princess, and how people will have different opinions about which makes a game darker. When I think of "dark", it's things that unsettle me - like violence - and things that are really depressing. Both MM and TP have elements of the latter, but to me, they never felt like they went overboard.
Really, I want complexity more than happy/dark. Wind Waker is a great example, when it goes from being a story about a boy and his talking boat to a surprise Hyrule history lesson. It also shows how other things can balance a game. They don't necessarily need to be "light" things like humor - let me go back to Axle's article again for a direction quote about Majora's Mask.
[I don’t think it matters how terrible the fear is in Majora’s Mask, because the acts of bravery, resilience and love by Link and the people of Termina overshadows – or should I say illuminates – the game’s darkness.]
So yes, my preference would be a game that is a cross between Wind Waker and Majora's Mask in terms of complexity of story. Considering the subject matter of Skyward Sword, however, I cautiously have my hopes up. Something that key to the entire Zelda series seems like it will have a great mythos surrounding it.