Yeah, Skyward Sword definitely bombed in Japan; and it's not that for big franchises Wii was dead, since Kirby sold almost 700k, and we had other cases where games sold remarkably well last year (Just Dance, Family Fishing, Go Vacation, GoldenEye).
And in the meanwhile, Zelda OoT 3D is probably approaching the 600k mark while we're speaking. So strange to see a remake outclass so much the next main entry in the series XD