I loved the game. 9.6 of 10 IMO. Here's a few gripes of mine. These may have been posted, I didn't read the whole thread. O well, more support if they have:
-I agree on having another couple dungeons. Nayru's Pearl DEFINITELY should have had a dungeon, and maybe a mini-dungeon or two could have been expanded into a full fledged dungeon or at least have gotten bigger. I don't care at all if it would've taken another month or so to come out since I just dust off the Gamecube whenever an AAA title comes out and spend 90% of my gaming time with online pc games.
-Bosses also seemed very easy, almost always didn't even need a fairy or potion! They should do something like twice as much damage as they do now. I want a patch err... this isn't Warcraft Expansion beta nevermind

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-Genral easiness all around. Nintendo probably didn't want the game to be too hard for the average player, the "Zelda vet" is in the minority most likely. I think I only died once and that was at the very beggining when I chopped up a pig so much it went postal and killed me... there was no way to get away! ah! Funny though.
-The stupid Pirate's Charm stone telling you almost exactly what to do and spoiling puzzles. Seems like sometimes I hadn't even been in a room a minute before the damn thing goes off, can't really ignore it since it is your A button... The "helpers" in later dungeons also give away puzzles. Guess they wanted to newbify the game some so begginers wouldn't get frustrated... yuck.
-The boat should have moved faster while sailing and cruising. Sitting there watching it take so long to get to a destination is boring. And yes I know you can teleport later on, you still have to sail quite a bit tough.
"--- The story was rather weak. I wish they had used more cutscenes explaining what the Master Sword is, why the Triforce is important, where Ganandorf came from, who the Goddesses are, why the Sages exist, and so on. They did this stuff in Ocarina, so don't understand why they skipped it here. After all, not everyone's played Ocarina. The backstory should have been fleshed out a little more." -good one here.
-The tedious/overly long "find the triforce peices" crap. There should have been something like only 5 peices. Would have been great if one was in a real dungeon too.
-The Redead ripoffs. They took the most annoying enemy in OoT, and just copied the same thing into Wind Waker. Bleh. Shoulda made a new "zombie" enemy I suppose.
Thats about all I can think of right now. Still a great game of course.
EDIT: Another thought: all the time they wasted on the "Tingle Tuner" to get people to buy a GBA was stupid. The effort should have gone into another dungeon, something everyone could have enjoyed. Who needs more help in these dungeons anyhow?