Nintendo designer Shigeru Miyamoto likes to base games on his interests and hobbies. Gardening led to Pikmin, for example. But what interest could possibly have inspired Zelda: Skyward Sword's unique art style?
Impressionism. Yes, Miyamoto tells Kotaku the 19th century art style, pioneered by French painters like Monet, is the inspiration behind the soft, warm colours (and wayward brush strokes) of Skyward Swords. Why? Because Miyamoto is a fan, that's why. This runs throughout the game, from the way you deal with enemies (whose dimensions and more importantly movements are visually exaggerated) right down to the game's sky, which Miyamoto says is a tribute to Cézanne.
If this all sounds a bit strange, take a look at the picture above, which is concept art for the title. Then take a look at some of these. Certainly beats "ruined factory" as inspiration for a contemporary video game, no?