Some more arguments:
Only one of the 3D Zelda games have given me enough dungeons...
I can play OOT for hours! The massive, diverse world! Forest/woods, large, breathtaking field, lake, desert, village, graveyard, volcano/mountain, another village, castle, river, waterfall, domain. So many towns! Kokiri Forest, Kakariko Village, Goron City, Gerudo's Fortress, Hyrule Castle Market, Zora's Domain, etc. So many places with so much to do! WW had what? Outset and Windfall... I can play OOT for hours, just walking around. tWW is just dominated with tedium.
THESE WERE NOT TAKEN FROM ME, BUT FROM SOMEONE ELSE!!!!!!!! I agree with him!

"wind waker was a slap dash attempt at a game, it was generally poor in every aspect. It deserves to be placed between 50-100 not number 1, that is clearly just bias. If anyone begs to differ, I will gladly debate why it doesn't belong in the number 1 spot.
Your first point on popularity: It is a leech game. It is leeching off the success of its predecessors and is gaining the support mainly from the fanboys. If you say that WW is the best game for the GC on the market, I may as well chuck the GC in the trash. I strongly, and I mean very strongly, believe that SSBM was a far superior game, it should be considered the best game on the GC to date. It came out with the release of the GC, reducing waiting periods, it promised a lot and gave a whole lot more, the graphics are so fluid for a 4 player fighting game, it is still very innovative even though we have all played the old SSB (which seems like a completely different game). There is so much in this game, and such close attention to detail, that this game easily gave me many hours of fun, after more than a year of having the system I still play it. Unlike the WW.
2. Compared to Ocarina...
Other than the bright colours, WW has nothing over Oot.
3. Graphics
I had no prejudice against cel-shading before playing this game, I hadn't seen any games with it used yet. But after playing WW, I thoroughly dislike cel-shading. There is this stupid annoying blob of hair that looks like crap, once i noticed, i couldn't stob noticing it. It looks completely rubbish. Everything is just an outline with a fill effect, someone could make this game in flash. If you want to see facial expressions, play Final Fantasy X, there may be a slight jittering problem (not as an advanced system) but it is clearly using the capabilities of a facial expression engine. The characters express a whole roller coaster of emotions in that game. In WW, all that was offered were 2 or 3 different facial expressions, one angry one sad one normal, and maybe 1 or 2 others that weren't that powerful enough to make me remember it. And they didn't even ease into each other, the expression just changed like his face was a powerpoint presentation.
There are without a doubt games with better graphical features, Kingdom Hearts easily beats any game in the colour department, while games such as Resident Evil and SSBM are far superior in general graphics.
Plot / storyline...
I'm pretty sure GTA was not meant to have a proper storyline, it is derived from a car game that has some very innovative features, that is why it is so popular. Wind Wakers storyline was poor, it was very poor. The so called twists could probably be worked out before you even start playing the game. There was no depth, or intricate themes or anything, it was so bland and re-used. If you want a good, interesting storyline, play a Square game. Even if someone were to say that a storyline doesn't matter in WW, it did matter in the previous zelda games, and like you mentioned it is dry. I would have preferred to have versed wave after wave of enemies (that are half decent, because all of them were push-overs in WW) than waste time listening to that woeful storyline. Kingdom Hearts is a good example of an adventure game with a good storyline.
Sound
The Sound 'sounds' better because the GC is an updated system, the N64 couldn't express Saria's song, which in many people's opinion is the best song in Oot, as well as it could have done because of the system's poor sound quality. However SSBM did do a good job with its remastered version of this song. The Wind Waker had no memorable tunes, I wasn't rushing off to a midi website to get my copy of the music. This just shows how unimportant and unimpowering it was. It was Truly forgettable.
Also, some of the sound effects were reused from previous games and were quite annoying.
THE BOAT
Who ever came up with this idea needs to be shot:
You had to constantly control the wind with the stupid addition of a conductor baton, which did i mention was very lame. The music it made sounded so off. If you over shot an Island because you were travelling fast or didn't see it because of the expansive stretches of blue sea them you had to change the wind again. You travel so slowly against the wind, and sailing with the mast down. It was only convenient for you to eat while sailing BECAUSE it took so long. The game enoucrages you to explore other islands yet all the optional islands are a complete waste of time going to, simply because it takes too long to travel and all you got was something crap like a joy pendant or a heart piece, I mean, why would you want to make an easy game even easier by getting more hearts? The world is just one island that was smash into little pieces and spread over an enormous map so it took the player ages to get to so the game seemed to take longer to pass. If I took the amount of time spent sailing and exploring and other useless side quests out, I could easily pass this game in a few hours, even if i had forgetten how to do everything.
Enemies
They all sucked, there was nothing at all hard about any of the monsters or bosses in this game.
Replay:
After I passed this game, it has collected dust, what a waste of money. I have not once had the urge to replay this game again
I have not really decided upon my personal favourite game of all time, I have games that I hold in higher ranks than others. Many of the Final Fantasy games are obviously loaded with effort when made, and I admire that, However I am annoyed when games make some slap dash attempt and it shows, these include most of EA games' games, starfox adventures (even worse than WW) and WW.
But for anyone who thinks otherwise, you can keep debating if you like." `Queztalcoatl from smashboards.
I don't agree with him that the game was poor (it is one of my favorites ever), but it just had alot of flaws. It could have easily beaten out OOT and LTTP if only Nintendo spend some more time on it.