Skyward Sword: when the controls go out of alignment it's very frustrating. It's easy to center them, but when you're in a boss fight, it can be annoying.
Fi is also a bit annoying. You don't need to tell me that my health is low, my batteries are almost dead or that my wallet is full. Just a little too much hand holding for me. Other than that though, I really like the game as a whole!