Warning: Lengthy rant incoming.
Skyward Sword is hated because it's the shining example of how Zelda, a 3D game series in 2011, is perpetually stuck in 2002 and was so far behind the competition that it was almost the laughing stock of the industry for a while.
Yes, I'm talking about every single facet of SS, not just the gameplay and design structure, but its presentation, graphical style, and the way it was marketed.
1.) Presentation
Let's start with the obvious - SS is a 480p game in 2011 with a "compromising" art style that just takes the worst of both worlds between WW and TP and the result is that very few people are actually happy with it.
I don't normally complain that Nintendo refused to go HD with the Wii, because the best games for the console honestly didn't show how antiquated the Wii was at that point. Mario Galaxy and Mario Galaxy 2 look excellent on my 48 inch HD TV to this day, with the likes of Super Smash Bros. Brawl and Donkey Kong Country Returns looking acceptable as well. SS is ugly on any TV that's relatively modern. "But TP looks terrible on an HD TV too", you might say. The difference is that TP was a Gamecube game in 2006 that got ported to the Wii in 2007 to help sales of a new console. SS is a whopping five years after TP finished development, and the result is a game that looked so antiquated right from its initial release that you can't look over that when the competition had games like Metal Gear Solid IV as early as 2008 and Final Fantasy XIII in 2009. Mario Galaxy looked fine. Donkey Kong looked fine. What's Zelda's excuse?
That excuse is its miserable attempt to find the "sweet spot" with the series' past contradicting art styles. I will never for the love of god understand why Zelda must constantly contradict itself with its moods and themes on a game-to-game basis. Mario knows what its art style is, Final Fantasy knows what its art style is, even Sonic the Hedgehog knows what its art style is. Zelda does not, plain and simple, and SS's attempt to somehow find a compromise between TP and WW yields some horrific results. The only thing SS takes from TP is more realistically proportioned characters, ditching the cartoon balloon-heads from WW. The rest is attempting to slap WW's rainbow-bast shading onto these now realistically proportioned humans, which leads to two contradicting foundations of the art that aren't an homage to a past style, or something radically different and new; it's just a soulless combination of what we had before, and in the event that you weren't a fan of just one of those past styles, you're going to be disappointed. This is, by definition, the worst of both worlds. Add that on top to it looking so horrible on any TV bigger than 20", and it's a recipe for disaster.
Also, the fact that voice acting was completely lacking in a supposed "narrative-based" game is beyond embarrassing. Yes, I'm going to keep bringing up Metal Gear Solid and Final Fantasy, because SS was supposedly competing with those games when it came to having engaging gameplay on top of a note-worthy story. This has been a problem since WW, and something that, in 2011, is inexcusable. If this game is being marketed to me as the prequel to the series, where everything starts, I expect high production values that get me emotionally invested in the story. Without it, I just have soulless text-bubbles that tell me what I'm supposed to be feeling, but which lack any means to actually do so.
And no, not having voices is not part of the "Zelda charm"; it worked back in OoT and MM when this 3D adventuring thing was brand new and we were all amazed by the environments you could have on top of interesting gameplay concepts, and when the story wasn't exactly trying to be super duper epic. If I'm comparing SS to the likes of MGS and FF though, it's laughable how much of a better job those games do at actually making me care about anything from a story point of view just because of their emphasis on actual character building that isn't the stereotypical "bully becomes friend" arc that Groose had (which is the only "character development" in the game at all, and I use the term loosely).
The music was fine. I can't remember any theme from it except the Ballad of the Goddess, but it wasn't bad or anything. So I guess that's something.
2.) Control
Many people claim that SS's method of control was fine and yielded absolutely zero issues for them. I'm not one of those people. Never mind that I think motion controls in Zelda are stupid regardless of how they're implemented (it's the reason I can't stand the Wii version of TP), but I just had problem after problem with it. I realize this is subjective and different for each person, so I won't harp on it too much, but did we really need harp segments and things like motion controlling for underwater? I had an absolute miserable time during both of these, because I just couldn't get the stupid remote to do what I wanted. This was especially apparent during the later harp segments, and nothing annoyed me more than loosing all my progress while having to listen to Fi's ear-grating "singing" due to the controls just not working for me. Other people have mentioned the swimming, and I'll just echo that I have the exact same concerns.
Aside from that, what practical design purpose were the motion controls needed for specifically when it came to improving the Zelda experience? The answer is absolutely none. You could take away the motion controls from SS completely, and the experience would hardly be any different at all except for a little bit when it came to how they arbitrarily used it for combat. What puzzles were completely impossible to design without the motion controls? What types of transportation could only be done with the motion controls?
You'll have to reach to find an answer to either of those, and for most of them, you'll find that the motion controls actively detract from the experience. Yeah, I'm sure we all loved how necessary motion controls were needed in order to control the birds in the sky. That example alone is enough to prove to me that they weren't worth it, and made the game worse in a lot of areas. This same thing applies to the multitude of puzzles that the game throws at you. There's nothing new that's actually new from a design standpoint; it's all rehashed material that's supposedly fresh because I waggle around a remote to solve it instead of using traditional inputs.
Look at Mario Galaxy. The motion controls in that game are so un-intrusive that you kind of forget they're even there after a while. All you have to use them for during a majority of the game is a brief shake if you want some extra air, and pointing at the screen if you need starbits. Neither of which are even required to get past any given obstacle in a level if you're good enough with the controls. SS is the exact opposite of this, thrusting on motion controls at every conceivable point so you don't feel like you wasted money on the motion plus peripheral.
Even with combat, why did something that wasn't broken need to be fixed? Was anyone really complaining about what WW and TP (Gamecube) gave to us from a combat point of view? WW had the parry system and the multiple weapon system, TP had the hidden skills, things like that. SS didn't need motion combat in order to build upon its predecessors and possibly make the best combat style of the series. The answer to this is that, just like with the graphic style, Zelda is like that one kid in high-school you knew.
You all know the one. SS is that loner kid in high-school that was so desperate for attention, he would wear the most outlandish outfits and hair styles for no reason, but just for the sake of being different. He always hoped that people would comment on it so it would make him feel special, but for the rest of us, all we gave him was a nervous smile and maybe an equally nervous laugh. He was funny for the novelty of it, but one that wore off, all that was left was this eyesore that you'd rather not look at. That's kind of SS in a nutshell.
3.) Gameplay
SS reeks of Mario Galaxy, and that's not a compliment.
It's so strange that Nintendo decided to completely abandon 13 years of design elements for 3D Zelda with SS. The very idea of a "hub-world" in a Zelda game is terrible, and yet, that's exactly what they did with Skyloft. I think they were under the impression that a hub-world was supposed to somehow supplement the lack of an overworld, but that mode of thinking is completely backwards. Just being in the position in the first place that you have to substitute something for an overworld means you've gotten a fundamental design principle of Zelda wrong, but it's insult to injury that the hub-world we got was lacking in just about every way.
I hated the boat mechanic in WW, and I hated the Great Sea in WW. But I would take that any day of the week over the mess that is Skyloft and the disaster that it is navigating it, trying to find something in it, and even just attempting to "explore" in it. At least with OoT, MM, and TP, the overworld was just a field at face value. Fields in real life don't have much to do in them, so you couldn't really expect all that much from it aside from a hidden hole here or a secret cave there. But with SS we're advertised that we have this entire world above the clouds with tons of things to do in it. And this entire world is supposed to act as our substitute for the overworld that has been a part of Zelda since literally the beginning. Even besides the fact that Skyloft fails on both of those fronts when compared to the likes of MM and WW, it doesn't even do a good job of pretending like it does. You can tell right from the beginning that all of the Skyloft islands come down to, "get item, find block, use item, get rupee". The lack of variety makes WW look like a masterpiece on the overworld front.
If you're wondering why I don't consider the levels below the clouds to be the "overworld", that's because they're not. They're Mario levels that are approached the same way you approach Mario levels: In a linear, progressive manner that presents you with linear puzzles that you solve in order to walk a bit further through the map. That's all they are, levels. This is such a problem because literally every 3D Zelda before SS had nothing like this. Lake Hylia in OoT wasn't a level that you progressed through in a linear manner, so why does Faron Woods in SS have to be like that? And this type of thing happens over and over and over. It makes them seem like pre-dungeons more than anything else, and there's nothing fun about puzzle-solving your way through a pre-dungeon before getting to the actual dungeon and having to puzzle-solve there again too.
I also can't stand Fi. This is coming from a guy who never really minded Navi that much, and who actually really liked having Tatl and Midna along for the ride. Those two did hold your hand occasionally, but the difference with them is that they had a, you know, personality. The things like that make characters likeable. Fi has zero personality, because she is, by admission of the developers, a soulless computer. Why on earth was that considered an acceptable companion for the entire game? She hand-holds constantly with completely nonsensical statistics that mean nothing to the player in any type of context, and her bland personality makes sure that every single interruption doesn't even have a slight amount of charm to it like we got with Tatl or Midna. She's by far the worst companion character of the series both on the front or being too annoying, and too anger inducing at the same time.
4.) Story
Zelda is not a series with a good cohesive narrative, and I don't think it ever was or will be. But the developers seem almost arrogant to the point of thinking that Zelda actually does have that kind of narrative going on that puts it on the same level as MGS and FF, and that's what annoys me; SS constantly seems to think that it's some kind of epic and grand tale about the start of everything Zelda, and it does little to actually sensibly deliver on that front on top of being kind of contradictory.
To start with, the Mario Galaxy style of progressive actively hurts it, I feel. We're supposed to be getting this story of how Hyrule was first created or some crap, but instead we're going back up to this sky town between every single little thing, and we're left confused. Okay, we had sky people in TP, but how can they possibly be related to these people? The sky people in TP were like little chickens, and we're not explained this relationship in SS. On top of that, the ending of SS suggests that a vast majority of the sky people came down to found Hyrule or something like that. And there had to have been a large population of people to found Hyrule or else there never would have been a civilization that we see in future games due to a limited gene pool. So where did the sky chickens in TP come from, and why are they still in the sky?
We're also supposed to get the origins of the Master Sword, where we find out that Fi was sealed inside of it for the entire series after SS. But THIS doesn't connect to any game at all, because there's never any indication in games like OoT or ALttP that indicates that some kind of spirit, let alone a major character, is a part of this sword. It's so arbitrary to introduce Fi as the spirit of the Master Sword in this single game when there is absolutely zero relationship we as the player of past games can drawn to said past games, and this is especially important because of the Master Sword's significance to pretty much every main Zelda game. I could have sworn ALttP or OoT or something like that actively stated that sages forged the Master Sword; there wasn't any mention of a sky person getting it and a robotic companion being the soul of it. How did the legend get so twisted to the point of being completely inaccurate on almost every level?
The one okay thing you could possibly have is the introduction of Ganon and by extension Ganondorf as a reincarnation of Demise. But doesn't this directly contradict what we learned about Ganondorf and his motives in WW? I'll be the first one to say that I despise Ganondorf's portrayal in WW and think it's a direct contradiction to OoT, but that doesn't change the fact that it's pre-exisiting canon. If Ganondorf is supposedly just a leader of a desert people who were being bullied by the wind, and his campaign in OoT really was just for the benefit of his people, how exactly does that tie into Demise's curse? The way Demise put it, his curse existed solely for the purpose of wiping Zelda's and Link's decedents from the earth. Why then in WW is this curse suddenly a sympathetic figure that we're supposed to feel sorry for, and who doesn't seem overly concerned with going after just Link and Tetra alone?
It's things like this that, when you think about it for a little bit, make Skyward Sword's self-proclaimed prequel status bothersome. It almost would have been better to just leave that story alone. Did we honestly need the legend of the Master Sword's origins to be explained? It seems so much more cool to just have it as this wickedly awesome legendary sword that was forged in the ancient times to combat evil, and that was so long ago that no one really remembers the specifics of it. Just things like that.
tl;dr I don't like Skyward Sword, and I hate it more and more every year when I think about it more.