I enjoyed The Wind Waker, loved Twilight Princess but couldn't really stand Skyward Sword that much. I do think The Wind Waker is the best of the three, though the graphics and themes of Twilight Princess come close. Skyward Sword seems like Frankenstein's monster, a little bit from the most recent games... Collect tears, like TP, while having Guardians (Phantoms?) chasing you, like in the DS versions. I don't know where all the "Greatest Zelda game ever" comes from. It's not near the quality, storywise, of any of the others.
Skyward sword is just so amazing. I love the water color theme. The storyline is the best storyline yet in the zelda franchise. TP is my second favorite. Midna was awesome and u grow to love her. Fi never had a personality.
SS was the best IMO, but if it wasn't for the very poor overworld design of WW it may have been different. I honestly didn't like TP at all -- the game was unnecessarily dark, the overworld was way too large, and the dungeons weren't that memorable. Graphics alone don't make a game great.
The only issue with Skyward Sword for me was the ending, it was a bit of a turn off. Also, not as many side quests, and the sky wasn't as vast as my assumptions. It felt a bit rushed... Whereas TP took A LOT of dev time, making it one of the best console games I have played.
But kids, never assume! It gets your hopes up... =w=