I would say because of unorthodox controls. I would much rather prefer digital buttons then motion controls. The vast landscape is kinda boring when you have to tread it more then twice and the flying in between them get is also a bother to people with short patience.
Skyward Sword is a game that you like or you don't like; I haven't seen too many middle grounders.
Despite the controls and some of the more annoying features, I enjoyed Skyward Sword as much as any Zelda game. Even though it gives the appearance of being repetitive, it did not feel that repetitive. Although that is a personal preference; I am sure others think it is quite repetitive.
The dungeons is what won me over to the game. The use of time shift stones and the Ancient Cistern were really creative. The Sky Keep is by far my favorite Zelda dungeon; it forced you to reuse all that you learned in the other dungeons and even added it's own twist to put them together. They managed to shove an entire dungeon puzzle into single rooms.