The only thing that really damned Skyward Sword was timing and expectations.
The usual "childhood memory" expectations of a Zelda game coupled with it being released as basically the final big Wii game was a recipe for trouble. It was unlikely that any game, even Zelda, could tear up the sales charts with Wii on its deathbed.
Nintendo went ahead and finished this game up because, well, it was all they could do really. Too much invested to "disappear" it, even by their standards of canceling / moving major projects. On top of that, the game does require M+, and despite the sales of Wii Sports Resort , Nintendo failed to make M+ a hot item with non-Wii Sports players. So too many potential buyers of Skyward Sword didn't feel like buying the game+hardware.
"That's why they should have done it RIGHT and had no fucking motion controls!" <-- this is the instant kneejerk response from the Skyward Sword motion control hate wagon as it passes by.
But that never could have happened, tho many people will drop dead before admitting it. Why? Because it's Zelda, ironically. It's the "native" Zelda for Wii, the game everyone expected years ago.
It seems many people have totally forgotten, after years of ingrained cynicism regarding "waggle" and the hardcore gamer's boogyman of 'casualization'. But turn the clock back to 2006, and you know what you saw? Nothing but excitement for potential. The potential of playing a Zelda game with "a real sword in hand". Stuff like that. One reason Twilight Princess was a let down for some people, at first, was that it didn't play like Nintendo promised and inferred Wii games would play. It didn't have "real" swordplay.
So people said "wait for the real Wii Zelda. Twilight Princess is just a port. It's a huge disappointment, but they'll make another Zelda." People were just angry that they'd have to wait years for the next Zelda, as is usually the case.
Fast forward back to 2011. Skyward Sword comes out, the one Wii game where Nintendo fulfilled their almost forgotten promise of the epic that made every use of the Wii's unique interface; the fundamental concept of the Wii itself.
But half or more of the audience (and potential audience) for the game approached it with years of hardened bitterness towards the 'plague' of motion control and 'gimmicks'. Regardless of how good or bad it is, how well it works, many refuse to accept that the game is exactly what it is because it could never have been otherwise. It had to be made, essentially; the long delayed validation of what the Wii was supposed to be at the beginning.
But it came too late; released into an environment practically designed to rip it to shreds for not being "conventional". (Imagine that.) On an end of life cycle platform. Requiring an accessory to play it, technology that should have been in the Wii at launch (and Nintendo knows it) that would have forestalled so many wasted opportunities and enabled the kind of games people thought they'd be getting right at the start.