Controls - they take some getting used to, but I never felt they were 100% accurate in the way a normal dpad+button setup would be.
Ocean Temple - worst idea ever in a Zelda franchise.
Smaller Dungeons - good for a portable game
Sailing - definitely much better than WW's
Puzzles - I liked the use of the 2 screens and it had a couple of head-scratchers, but nothing overly challenging. Using
spoiler (click to show/hide)
the rope as a way to bounce yourself up platforms was cool and creative.
Bosses - for the most part, easy, but cool and another one of the more creative aspects of the game. The use of the 2 screens on the Spider for instance.
Story/Characterization - Linebeck is the man, but the plot is your typical Zelda, go around collecting items stuff.