I honestly believe if there were any dent in the sales for the Skyward Sword, it had to be in the controls and the fact that it required wii motion +, how many "good" games actually require a add-on like that? Not many, at least from the list that I read. So in that case, most people (which I also know a few) decided on not buying it and go for another game (i.e. Skyrim) in its place.
Its a combination of competition from other games and controls that stopped Zelda SS from moving onward like the previous zelda games.