I am going to list everything I found bad about Skyward Sword. There is a lot more positive, again one of the best games this year, this gen, etc. It is still Zelda goodness. Its still the best mix of action adventure and puzzle elements of any game. Its a fantastic game. That said, now to nitpick it to death.

SPOILERS don't read this if you haven't played it, I talk about everything.

• Slowest text scroll ever. Other Zelda games text can move quickly, not this one. You will read this bitch! But thats not the worst part, its the damn repetitiion of text for every single item or store, its ridiculous. Oh and how the game stops to show you every damn treasure or bug after you restart the game, why, how does this happen, who programs this shit?!
• The game treats you like an incompetent idiot. I know Nintendo games want to make sure everyone can play their games but this is kind of overboard. There is already a built in help guide with the stones but Fi still interrupts you every second you need to do something. Then you have dowsing which will literally take you to where you need to go and the option to ask Fi for advise. Also everything you need to know is highlighted red to make sure even the stupidest person doesn't miss what they need to focus on. So much for figuring out a puzzle or quest on your own.
• The sky is a complete waste of potential and this is probably the single worse aspect of SS. Its empty, it's practically pointless. Compare it to WW which has a majestic overworld with so much to find and explore, this is so sad. We could have had a huge sky with tons of islands with things to find and explore. Or we could have had some form of bird combat, or arrow shooting from the bird anything to make flying interesting. Plus there is no fast travel so you have to fly everywhere, all the time, just fly fly fly fly across empty space.
• Quite possibly the best combat in all of Zelda but with the worst selection of enemies. Hey we finally have an awesome sword combat system lets remove the MAJOR enemy that sword fights you. Where are the Darknuts?!?! OMG they are so perfect for this game, who said not to put them in the game? Plus there are only like 10 Stalfos the entire game. Every enemy that would provide a great sword fight is removed or put in limited rotation. So what you get is a bunch of sword fodder.
• Items have almost no use in combat. Remember in TP where you have these bird things that have shields and you have to time your hookshot to take down the shield and then hit it with arrows. Or use the ball and chain to break enemies armor. None of that here. Certain enemies have a weakness to bombs and of course arrows but those are basic Zelda combat rules, there is no interesting use for items in combat.
• Speaking of items is the clawshot totally useless in this game? Its not used in combat. Its never used in any clever ways. There are always clear marked clawshot points with no real puzzles or even obstacle courses for it. TP had an entire dungeon designed around the clawshot, enemies made use of it and it was incorporated in puzzles like one that had me stumped for quite a while in dungeon 7.
• Puzzles are very simple. I was waiting for something, anything to really test me. To make me think for more than a minute. Did not happen. Either I am really good at Zelda puzzles or they didn't try hard enough, I know its definetly the latter. Almost all the puzzles are simple straight forward use this to make this happen. It never goes the extra step to where if you use an item something happens which causes something else to happen and then you need to figure out how to make both reactions work till you get the solution. I am not expecting Portal level puzzles here but I miss the puzzles of previous Zelda games where I would get stumped every once and a while.
• Repeating bosses. I hate the Imprisoned, I really hate it. I never want to fight it again. Everything else was fine but the Imprisoned was just too much.
• Side quests kind of suck. Again since this game makes sure to tell you where everything is side quests feel like fetch quests. They almost all involve simply getting item for someone and bringing it back to them. Then the game will give you a million obvious clues as to where this item is. Whatever happened to a character that would simply not react to your actions until you find a certain item that will get him to react, it was a puzzle in itself to figure out how do I help this character out. Here its all just fetch this and that.
• The economy is a mess and I don't just mean rupees. The bugs and treasures you get seem rare at first but after 25 hours I had everything upgrade and so many of these treasures I would never have to look for them again. But the game puts them in everything, chests, mini game prizes, enemy drops. When I have no use for all these things it really makes getting them as prizes pointless. Oh then there are the rupees, maybe I missed something but I think you get a wallet that holds 5000 rupees and there is not a single item in the world that even comes close to costing that much, then why give me a wallet that big?!??!!?!?
• Girahim is the worst Zelda bad guy ever. Just boring, crappy, annoying with no character arch at all. So many complain about seeing too much Ganon, well shut it,  he is a million times better than the stuff Nintendo comes up with now. It wasn't until he showed up at the end that Link finally had a good villain in this game.
• The story is a mess. Its the origin story oh but wait there are a million things that happen before this game. There are goddesses and demons and a giant war. The triforce fits in there somehow. The master sword gets created by some random fire, I don't know and what about the skyward sword, what made that? Eh whatever I don't play these games for stories but TPs and WWs story was a million times better.
• Lack of a true overworld hurts. I miss that feeling of riding out to the mountain in the distance. Of finding Lake Hylia in all its glory. Finding a city of Zora's under the sea. This game simply didn't have the same sense of exploration other Zelda games had. Repeating areas doesn't help either.
• The light cube and treasure chest system, terrible. Lets make the sky even more pointless, I just loved finding an island and finding out that it has a chest I can't open yet, yay! So instead of the process of finally getting an item that will allow you to reach that chest you so wanted, now you have to wait till you find some cube down in the world and then the game will tell you exactly where this cube is ruining the whole feeling of exploring for it. Here is how this should have worked, you hit a cube on the ground then one of those many totally useless rocks floating around in the sky transforms into a brand new island with areas and puzzles to solve.
• This is a positive at first, a random BOMBABLE WALL! OMG!!!! YES YES! Oh its only done once the entire game. Fuck you. They set it up and everything, oh there is a wall that is bombable, search for wind. I thought the rest of the dungeon would have random walls you need to find to bomb like Zelda games of old, nope. Again the game tells you exactly what to do.
• Swimming controls, who thought  that would be a good idea. Analog sticks are better for movement, period. It works great for the beetle though since that is an item and part of the trick of it is getting it to fly properly.

Thats all I can think of right now. Yes its a pretty big list but again its stuff I would gladly put up with for that Zelda design goodness. The major issues that are worrisome to me is how the puzzles seem to be getting more simple and how the game handholds more than ever.