First and foremost, I dig Link's Awakening above all others, though I, like many of you, am a die-hard fan of all the games. What stuck out for me was the storyline in the game, how it didnt take place in Hyrule, and the whole Windfish idea. If you beat the game, you know what im talking about. If you didnt....Well, go play that game and beat it.
And what was so great about Wind Waker? What -wasnt-? Okay, if you didnt 100% the game, youre missing out on a ton of stuff. The whole Pictobox dealy, all the submarines, finding all the treasures buried at sea, getting all the squares of the map, getting all the heart pieces, finding -All- the fairy fountains, the merchant subquest, the picto subquest, the various odd-jobs you can do around the towns, the spattering of minigames, the 'extra' items you dont need but can still get..
To my knoweldge, theres more than the four dungeons, too. Theres Dragoon Roost Island, Forbidden Woods, Forsaken Fortress, Hall of the Gods, Earth Temple, Wind Temple, Gannons Tower, and theres likely one other i'm missing.
Ontop of all of that, as Sabia pointed out, the story is badass. What remains of the world, 400 years after the events on LoZ:OoT? How is that not cool. The whole legend about Link and everything, magnificent. 'The boy clad in green clothing of the forest who appeared out of nowhere and slew the fiend'.
Anyways. You should really take a second look at the game. But Link's Awakening was a sorrowful story, the ending made me want to tear up if I were capable of that function. Being a man, however, I am not. So I just sniffled and went on about my day.