The hardest Zelda dungeon for me would have to be the Water Temple from Ocarina of Time. And probably a bunch of other people are going to say this too, but that is because it probably is one of the hardest dungeons in Zelda. If I could say another one, though, it would have to be Great Bay...
I can understand why Nintendo did it this way: because if they just had 2 splits, it would be too confising to try and put all the games into two splits.
From what i have watched, i think it is a pretty good game. Different, but good.
I have only played MM, but i have watched LPs ob a bunch of other games and SS looks awesome in every factor: graphics, music, story, controls(from what i have heard).
Mine is the block puzzle in MM in Stone Tower Temple where you have to flip the room upside down and rightside up to get the block to the other side of the room.
Favorite Zelda Enemy
My favorite Zelda enemy by far is Goht from Majora's Mask. I think that the way you battle him is very unique: rolling at him as a Goron. Plus, I think it is kind of ironic that he was the one creating the winter in Snowhead, yet he froze himself!