**Mild spoilers about Wind Waker's puzzles follow...I think I was vague enough that no-one will care.**
It's true that we take certain Zelda puzzles for granted. I played Wind Waker with my girlfriend and she had no idea how to get through the very first room in the Dragon Roost dungeon. All she had to do was light one of the sticks on fire and light the other torches with it, but this is completely unintuitive to someone who hasn't played through the other Zelda games. It struck me as she spent several minutes trying to figure it out that I might as well tell her what to do because she didn't have the slightest idea. Some of us have been doing it over and over since A Link to the Past, but it's nearly impossible to a newbie. I'm guessing King of Red Lions might give you a hint if you take forever in that room, but I've never waited long enough to see.
What I found ironic was how the game spelled out the rather simple candle puzzle in the final dungeon. Anyone who's made it that far in the game has figured out harder and less intuitive puzzles, to the point where I knew what I had to do before I had even seen both halves of the puzzle, yet they spelled it out completely by showing the things you had to do in order.
So I guess Nintendo needs to try and come up with some new types of puzzles. I think Nintendo's really good at puzzles, actually. Even the bosses in the Zelda games are puzzle-like, they're really outstanding, usually.