Story-wise it was pretty boring. Nothing happens. "But how can you say that?" Well let's look at Ghirahim. What does he do in this game? Nothing. He just pops out after every dungeon apparently being busy. Ganondorf and Zant were way more antagonistic and involved in their games (when I refer to Ganondorf I don't mean Twilight Princess). Ghirahim was just some sort of pest.
Without a real villain there isn't that much tension to your actions. The game is all about chasing Zelda. It mad me feel like I was just going through the motions. I wasn't doing stuff because I was being told to.
I think the problem really has to do with how the story is designed around the game's quests which rely too heavily on fetch quests. You can't deny it. There's a whole mechanic for the purpose of searching for things. This Link feels like an errand boy.
But... when the story actually delved into the lore instead of just advancing the game it was actually pretty interesting. The revelation of why Link and Zelda are constantly reincarnated was fun. Demise's reveal sort of makes Ganondorf less of a villain since he's just a part of Demise's destiny as opposed to his own. And okay Groose was great. He became such a likeable character.
Anyway back to the game. I'd say Twilight Princess is the better game for me. And don't bring up any nonsense about the "Zelda cycle". My two favorite things about Zelda are dungeons and exploration. I was harsh on Twilight Princess among other things because the game was really lacking in the mini-dungeons, especially coming from Wind Waker. But Skyward Sword is even worse in this. There is almost no reason to explore outside of a few out of the way cubes or meaningless treasure chests. Skyloft is empty and Goddess Cubes explicitly tell you which chests they unlock. On the ground, you don't need to explore because anything meaningful will be opened up to by the story.
Why I think Twilight Princess is better is because at least it had some side-dungeon-like levels and the dungeons were complex. 1 out of 2 for Twilight Princes. Skyward Sword's dungeons feel really simplistic. Almost every room feels self-contained and flat. Rooms in Twilight Princess were multi-levelled in a meaningful way. Skyward Sword, not so much and if it was it was only for a single room puzzle. Because of this you could clearly see that the game was designed by the portable teams. The portable games are very flat. What you do on one floor had little effect on the others. It's not bad for portable games but for a console game I expect more. Really I think my favorite dungeon of the game had to be Lanayru Mining Facility.
Controls for the most part were great though. I'm a full believer of motion control gaming now as an alternative input. I realized this during Fledge's pumpkin shooting mini-game. It just felt natural. With analog controls I feel like I'm dragging the reticule but with motion controls I just move and the reticle reacts instantaneously. Outside of the jabbing and unintentional spin attacks I felt the combat controls were perfect. I don't care if combat flow became slower because it at least felt more involved.
Other flaws like the treasure reminders and how meaningless the material system have probably already been talked to death so I won't divulge into it.
Fi was meaningless. I'd say rewriting her out of the game wouldn't change it too much. She just doesn't have any affect on the game. She's like the opposite of Midna. Midna and Link bonded and the whole story was based around her and overshadowing Link and friends. While in Skyward Sword it's all about Zelda and Link.
I think Wind Waker's art style is still better than Skyward Sword. Both were definitely used to hide the technical limitations of the hardware they were on but it felt more necessary for Skyward Sword than for Wind Waker. I think it's because Wind Waker embraced its art style (with wacky animations and lots of exaggeration) while Skyward Sword was more toned down. It does feel a bit like a reskinned (but also slicker) Twilight Princess.
Music was less memorable and more ambient. Even though a lot of people gush over that type of music in games and films I prefer more catchy melodies even if they're less complex.
I still had a lot of fun with the game. I don't think it's groundbreaking for the series. It lays a good foundation though and I'd be happy if this formula replaced the old one if they cut off a bit of the fat and made the game more complex.
Oh and Ghirahim =
Greed