For Zelda games, I really only find it interesting to compare games within the series; Zelda games in general are awesome and tend to do most everything right, but vary slightly from game to game. So I mostly judged this game compared to some of its ilk like Ocarina of Time, Majora's Mask, and Twilight Princess.
Compared to those, this one held up pretty great. It created a very nice fictional world, had some very memorable characters, good weapons, dungeons, new ideas (like timeshift stones), great music, and generally is just a kickass Zelda game.
For things I think it did very right: the story, the characters, the cinematography, the baddie, and item upgrades.
The Story.
Wow, was this satisfying. Granted, this mostly concerned Zelda, so Link is unaware of the story most of the game, but towards the end things start to come together. It becomes more than just "Save the princess, save the world." It actually tells a story. And what's more than that, it's not just about Link, he's just a part of it. One could even say he is only half of the story. The rest of the story, Zelda's half, really felt refreshing and alive. It gave that such a sense of purpose when finishing the game.
The Characters.
Along with the story, the characters were just really well done, especially Link and Zelda. Yeah! Link! I mean you can only do so much with a mute, but it was mostly how invested in the story he actually is. He wasn't doing it because he was the chosen one, he was doing it for his friend. And Zelda, well, lone gone are the days where she is merely a damsel in distress. She literally has her own adventure apart from Link, one that is actually crucial to the story. More crucial, some would even say, than Link's.
Some other characters, like Groose and Impa, were refreshing as well, with a bit more life than ones from games past. And of course there was no supply of the other misc. civilians, most of whom were quite memorable.
The Cinematography.
I noticed while playing how much they were trying to make it almost like a movie, in the sense that everything told a story. Cutscenes like Link slowly descending into each new dungeon he discovered. It wasn't super strong, but it was enough to make me feel like I was truly hearing a story -a legend, even- rather than just watching scenes strung together.
The Baddie.
Ghirahim. In a lot of ways, he's similar to Zant from Twilight Princess: he's a pawn, he is cocky, and he's crazy as all hell. But he's different enough. I love that you meet him several times throughout the game rather than just at the end. He wasn't shrouded in mystery like Zant, you got a chance to see him slowly unravel at the hands of what he viewed as an insignificant bug. It made the hatred he feels towards you at the end that much more real. I can't justify everything about him, like his fashion sense, but he played his part well.
Item Upgrades.
This wasn't huge but I did like the ability to upgrade items. It took away a little of the extreme linearity of some of the past Zelda games. I am not sure I'd want them going all hardcore RPG on me in future games, but Skyward Sword's amount was great and I hope they keep the idea in some form for later games.
For things that I found lacking: the hand holding, the sidekick, the overworld, and the motion controls
The Hand Holding.
I was just kind of floored at how much this game tries to hold your hand. Most of this is done through Fi, the companion, like jumping up immediately after talking to someone to tell you what you just heard, but it's also more than that, like having an annoying glowing, beeping C button every time you learn a new dowsing target. I understand how dowsing works after the first time, yet the beeping will not stop until I view the new dowsing target. The other big thing I remember is how the map would painstakingly zoom in to where you are and then hold there for several seconds. Like you don't know how to check the map from the item screen.
Basically, there were many times in this game that I felt it treat me like an idiot, and that's not hyperbole. Like if I'm able to understand how to beat boss X or solve puzzle Y but cannot understand that I have low health, the game must think I'm an idiot to have Fi remind me. And please, don't get me started on her "Master, I calculate a 76% chance that the obvious thing you need to do is what you should do."
The Sidekick.
As I already mentioned, Fi was guilty of much of the handholding, but that's not the only problem I had with her. Mostly, I found Fi boring. She isn't even really a character. I understand, she's supposed to be practically a robot, spouting out statistics and being all Spock-ish, and I accept that. But if you're going to make your character that, at least make her interesting. Maybe this was just her contrasting how well the other characters were done, but she just doesn't have a personality. Spouting statistics isn't a personality. Dancing around and jumping into the sword isn't a personality. Everything she did felt like she was performing a subroutine, not coming from her personality. Even the final scene -which many people said was heartwarming- I found boring and did not really change the way I saw her. (Though it did change the way that I view the Master Sword, but that falls more under "Story".)
I'm not saying that I expect her to be a phenomenal character; I understand her purpose and it's not like Navi or Tatl had me super attached. If you want to make her simple and robotic, that's fine. But if you're going to make a character be the babysitter for the player, make her interesting too, otherwise she just comes off as annoyance incarnate.
The Overworld.
I felt this almost immediately: clouds are boring. I can't fault them too much because I really liked the idea of having a world in the sky and the world below. They didn't have much choice, but that doesn't change the fact that it's hella boring. This isn't a huge deal, but I can certainly say that I enjoyed the overworlds of OoT, MM, and TP far more than flying in the direction of a light. It's just simply unmemorable and not "fun" in the slightest.
The other parts of the world were stupendous though so I could have let this slide, if it wasn't for the motion controls of flying. Which brings me to the next point.
The Motion Controls.
By far the worst part about this game. I'm not a fan of motion controls to begin with, but I can firmly say that they were far worse than the motion controls in Twilight Princess. I understand that many, many people say that they never had any problems and I believe them. But all I can say is, I was not so lucky. I don't know if I was standing too close, if I had a defective Wiimote, or maybe it's because the sensor bar isn't the official Nintendo one. All I can say is that it sucked a lot of the fun out of the game for me.
At times this almost made the game unplayable. I had to realign the pointer probably every 5 minutes, probably even less. Multiple times in one boss fight. I would constantly die from it not reading what I was doing correctly. Nothing insane, a vertical slice. I would stand there, doing a vertical slice multiple times, and it would either not register any of them or register them as a horizontal slice. It made even killing a Deku Baba extremely annoying.
And that's just it, it wasn't because I just wasn't playing good enough or couldn't figure out what to do, I literally could not get my character to do what I tell him, even in the simplest of tasks. Flying was one of the worsts, which is one of the reasons I hated the overworld so much. Any time when I had to fly with any kind of precision at all, the controller would freak out and send me veering off in random some direction. I would try to regain control and nothing happened. Ultimately I would have to just drop the Wiimote to my side then point it at the middle of the screen until my Loftwing decided to stop spazzing.
I could keep citing examples, but the point I'm trying to make is that this was persistent, constant, and extremely annoying to the point that I simply did not enjoy many parts of the game. It's an entirely new type of frustration. It isn't the level design being too cryptic. It isn't the game relying on cheap difficulty. It isn't monotonous. It's failing to adequately perform basic movements. Dying not because you timed something poorly but because the controller registered a stab as a swing. Having absolutely no idea how to even control your character because the callibration is off and you have no idea where the "center" of the screen is.
Simply put, it's maddening.
However, even with all that ranting, this is still a superb game and I would heartily recommend it to anyone who likes video games. The motion control did make it less enjoyable for me, certainly, but that mostly just culminated in shorter play sessions and more cuss words shouted aloud. All the other gripes were really just complaints rather than flaws. The end of the game still left me feeling content that I had experienced it and fulfilled as only a great game can do. And I really can't fault it for my own personal control debacle when so many people -including my brother- say they never had a problem. So I'd still say this game ranks up with all the other Greatness that is the Zelda series.