A lot of the things I have to complain about have already been noted in this thread. I'll start with dialog and info boxes. Fi was a dry terrible character which I felt really had nothing to do with the story of the game. Midna was probably the most interesting companion in the series. I was hoping they would stick with that when making new games, was Midna an asshole... yes she was. But at least she developed character as the come went on. Going from someone just using you to reach her goals, to someone who is on the adventure WITH you. Fi on the other hand is nothing but a tutorial guide that really had no use after about 30 minutes of playing the game. She constantly inturrupts your game to tell you meaningless BS that you already know or could have went without knowing. When Midna did this at least when she was talking too you she had character, sometime joking or being a smartass. With Fi, if she has something to say, you must listen, even if it is in the middle of combat. This is also something the game itself is guilty of as well. You could be in the middle of combat and upon defeating a foe, you will pick up a collectible, and literally in the middle of a swing of your sword, it has to stop and tell you that you have a bug, and its story and background. I mean really, its an effing bug, who give a flying *&#! about a bug and its background. But as if it wasnt bad enough that they stopped the game to tell you about it the first time, I tells you every time you pick up a bug (granted its a different bug, or you had saved the game and played later). This is present in other instances of the game, but I'm sure I made my point.
This will be a short sweet explanation, while the motion controls seemed like an interesting Idea, it was used in a stupid way. Zelda is meant to be a core game in the Nintendo library of said system. Normally put out as the pinnacle of what that system has to offer. But as Crimson mention, Skyward Sword was used as a Tech Demo to show off what you could do with the Motion+. And as if that was not bad enough, they didnt even work. The most evident instance I notice was when the Lizard enemies would taunt you and you have to swing diagonally, but it never works. So that is very annoying. The only enjoyable thing about the Motion controls was the fact that you could roll bombs, I actually think that was the coolest part of the game.
Story wise, I feel the game failed as well. It was hyped as the game that started it all. The origin of the Master Sword. When really it didnt tell anything about it. Maybe I missed something. The only link I seen was that the Goddess Sword started to look like the Master Sword, and I can see how it was named, as Fi always called you "Master" hints the "Master Sword". The story itself lacked any lore or recognizable info relating to the series. Ghirahim was a good character, very interesting, as well as being more threatening not cuz of his size or strength, but because of his extremely disturbed personality. Then to find out that the completely absurd stuffed animal (The Imprisoned) was actually Akuma and the main villain of the game in the last 10 or so minutes of the game almost seemed like a slap in the game to the player. I enjoyed the relationship between Link and Zelda, but that was still very minor. Impas stern attitude towards Link was cool, with her thinking that you were no where near worthy for the quest that you were on. But seriously that was very little in the way of story telling.
But most of all I hated the over world. Having a hub connecting the world is just out of place in the Zelda series. There was no real sense of exploration as the provinces of the world were completely disconnected. Zelda is a game where exploration was at the forefront of adventure. Being able to traverse the entire world seamlessly from one area theme to the next. Instead you had 3 different areas almost set up as levels instead of being another part of an expansive world. If you want to explore a different area of the map you had to return to the sky, soar through the empty sky and descend into another section of the world. There is the key word, "sections". The sky had all but nothing. little floating island that served little to no purpose outside of holding a chest that was unlocked by a cube on the surface. Even worse upon finding the cube, it was marked on you map. Not to sound cliche but the game held your hand throughout the entire game. All but giving you the solution to every puzzle in the game. The overworld is the utmost worse aspect of the game. Completely breaking the best feature of the entire Zelda series, as if it wasnt bad enough that Twilight Princess was an open world that consisted of a series of lanes and paths instead of an open world of choice with numerous ways to reach said destination. The only thing I liked about it was that entering a dungeon was a puzzle in itself.
While SS is not a terrible game, it is by far the weakest entry of the series. The entire game was nothing but a gimmick. Gimmicks are okay if they are just part of the overall experience. But when the game is based around the use of the motion controls, it is then just a glorified Tech Demo, lacking story, and reason to continue the quest. There was no sense of impending doom, like say Majoras Mask was a champion of. The Hype Nintendo pushed on us for the game was completely unjustified in the end. Maybe Nintendo was guilty of their own demise when it came to Skyward Sword. The game just lacked a lot of things that makes Zelda so great. In the end completely causing the game too fall flat of anything amazing considering its unacceptable development time. So heres to hoping Nintendo will learn for the travesty that was Skyward Sword.