I would never say Skyward Sword is a bad game by any stretch of the imagination. It is one of my least favorite Zelda games though.
The motion controls often register incorrectly or don't register at all.
Many of the enemies are boring games of simon says.
Almost every sky island is empty, aside from treasure chests which you can't access unless you activate them from the surface. Why not just put the chests on the surface instead of forcing the player to tediously fly to them? What does that add?
There's barely any exploration.
The side-quests seem like something you'd expect to find in an MMO.
All of the The Imprisoned fights are annoying and devoid of fun.
The game outright tells you the solution to puzzles.
The harp is awful.
The upgrades in the game are pretty much useless considering the game's so easy (if you disregard the flaws in the controls, which adds some bad difficulty).
There are some good nuggets thrown in there, like the time travel crystals, which were a great imaginative mechanic, but overall it was absolutely a bad game and it makes me uneasy to think that Nintendo could make something like that. Players need to raise their standards. We aren't going to get better video games otherwise.