I'll admit, I was one of those people who wasn't sure about the cel-shaded graphics but now they have grown to me. I love the realistic style of Twilight Princess, but I can't decide now which is better.
It has been stated before that the art style itself depends on the mood and the feel of the game. That's why it's always changing. If a game is more serious and gritty like TP, it goes for a more realistic approach. If it is a lighter feel like in Wind Waker, there will be more brighter colour and more emotion. But in the end, it doesn't matter too much to me, as long as the graphics are done nicely and don't look horrendous.
The art style for Skyward Sword was picked to help exaggerate certain things in the environment and on the enemies. As for its mood, I'm thinking of something in the way of OoT- a bright sort of game with perhaps some dark elements as well. But that's a topic for another thread.