Ganondorf's personality in this game is widely praised for giving the Thief King more depth and even lead to some sympathy for him. But, this was not only an extremely intriguing development of his character, it was necessary for his goals. It was stated in Ocarina of Time that the Triforce was split because when Ganondorf touched it, his heart was out of balance, seeking Power above all else. So he spent his time in exile contemplating where he went wrong. He gained the Wisdom of personal insight, analyzing his own motivations, acknowledging that it was his own envy and greed that drew him to seek Power. And when confronted with the reincarnation of the Hero of Time, he knew he had to fight with Courage, disdaining his magical abilities and transformations to fight him on equal ground (why he has become such an excellent swordsman). He has trained his body and meditated on himself so that when his plans finally came to fruition, he could make his wish on the Triforce, and not have it scatter. Too bad the King touched it first. (Who possessed the Wisdom necessary to make a Courageous, self-sacrificing wish for the Power to defeat Ganondorf once and for all.)
Why the Earth temple is so scary and haunted? Easy, the whole area is a burial ground/catacomb system. And Link is profaning it!
The photographer guy on Windfall Island says it's his hobby to sneak up behind people. This is actually a very good skill to have if you're a photographer, and you want to take candid shots without people noticing you're doing it.
Northern Fairy Island. There's a rich looking man on the island, using a telescope. Now, the upgrade you get here is one of the Wallet Upgrades, and the only house on the tiny island was the aforementioned Fairy Seashell house, which has no puzzle to get in. The rich-looking man probably just stumbled in there and got the upgrade, though you don't get the wallet full after the upgrade, which arose even more Fridge Brilliance. He probably was a sailor as well (seeing as Link isn't the only person on the sea), and he traveled to Bomb Island, another area he is seen in, and bombed all the rocks, all but the one at the top, have rupees. He probably did this for hours, seeing as you can escape from the hole and it resets them again.
Ganondorf duel-wielding. The only other Gerudo note Not counting TP Ganondorf we encounter in a straight-up sword fight are the women guarding the carpenters in the OoT's fortress — who also use two swords. Either the WW sword fight was a Continuity Nod, or the Gerudo generally dual wield.
Zora and Ritos:
On a similar note to the above, the Ritos' reliance on a scale for their wings makes a lot more sense when you remember signature items of the Zoras'— the Silver and Gold scales. It might not clear up the evolution issues, but it has a certain symmetry to it, looking at it that way.
The evolution issues could be cleared up when one considers why the gods flooded Hyrule: to keep Ganondorf trapped down there. In order to prevent any Zora from diving down deep enough to discover the old world and risk freeing Ganondorf, the gods took away their fins and gave them wings.
Of course, flight and swimming are very similar processes, so the change is less drastic than one might imagine.
This makes even more sense when you consider that Laruto is Medli's ancestor.
So, on average, we agree that Wind Waker Link can be rather clueless at times, especially when compared to his counterparts from Ocarina of Time, Twilight Princess, Skyward Sword and even his fellow cel-Links from The Minish Cap and Spirit Tracks. Stop to consider the fact that he's the only Link whose Exposition Fairy was a) not around from the start of the action note The King of Red Lions first appeared on Windfall, but he doesn't give any advice until well into Dragon Roost Cavern and b) one of the few who can't be contacted on a whim from anywhere on the map. Navi, Tatl, Midna, Fi, Ezlo, and Zelda would all talk to Link on a regular basis when he (apparently) asked for advice (Navi, Tatl and Fi in particular, could use an Enemy Scan) but the King was a boat sort of and couldn't follow Link through dungeons, caves, etc. In other words, WW Link had to figure almost everything out on his own — he's not dumb, he just had to use trial and error to work things out, on top of trying to stay alive until he did find the answer.
Also notable is the fact that he cannot possibly be descended/reincarnated from OoT-Link, since that Link stopped existing in that timeline when Zelda sent him back. So it makes sense that he would have a different temperament, as he's more of a successor than an heir. It also is consistent with the "forge your own path" theme of the game.
Another note about said theme: it relates to the reason that OT-Link was sent back: so he could live his own life.
On a note related to figuring things out, why does Link think he can just open the cell containing the three girls? Because the door neither has bars blocking it off, or a big ol' obvious lock the size of his head (or bigger than his entire body) in the middle of it. Okay, so a little thinking might bring him to the conclusion that a door to a cell that is holding prisoners wouldn't be so easily opened, but still... he comes from an island where anybody can theoretically enter anyone else's home at any time (in practice, only he seems to), so he doesn't have experience with locks like that.
The Koroks aren't just evolved from the Kokiri, as the Rito are evolved from the Zora. The Kokiri come from the Great Deku Tree in Ocarina of Time. The Koroks come from the Deku Tree Sprout in Ocarina of Time, which becomes the Great Deku Tree in Wind Waker. They actually come from a different family tree, so to speak.
When you first visit Dragon Roost Island, you can get Wind's Requiem immediately. Later, when you have to help Medli fly into Dragon Roost Cavern, you're supposed to wait for the wind to pick up and blow in the right direction. If you use Wind's Requiem, however, you can direct the wind as you choose and it will no longer change direction on its own. This initially seems like just a convenient little trick, until you realize Medli mentioned the "atmospheric currents are really messed up". By conducting Wind's Requiem, you've restored the atmospheric currents to their normal state.
A bit of Fridge Brilliance and Heartwarming for fans who have seen the ending of Skyward Sword. So, Fi and Demise are trapped in the Master Sword. Remember, Ganondorf is the (re)incarnation of Demise's hatred. However, in this game, Ganondorf has more or less let go of his hatred for Link and Zelda. His final boss battle is more or less a physical Madness Mantra due to being finally denied the Power of the Gods he so instinctively desired. When the Master Sword was placed rather firmly in his scalp, his thoughts immediately turned to home. He abandoned his hunt for the Triforce, he abandoned his hatred for Link and Zelda... the last remnant of Demise's hatred was gone. Demise would have lost his only bit of influence and vanished. Ganondorf died his final death. Fi would finally be free to move on to the heavens. Isn't that heartwarming?
So at the end of Wind Waker, the King exploits a loophole in the Triforce mythos. Ganon made his wish on it, but the first person to touch it gets his wish granted, not the first to make a wish. Cut to the King after Ganon has made his wish, and what's going on? The King has his hand resting on the Triforce. More specifically, the Triforce of Power. Except, it only looks like the Triforce of Power in the close up— when the camera pulls back, you see that he came into contact with the Triforce of Courage, which may have more brilliance behind it than the 'salt in the wound' from the Triforce of Power. For one, it's the piece that the King helped put together/watched Link earn, but he also demonstrates a good deal of courage in the ending, when he stays behind in the flooding Hyrule.
Mila's father is made out to be a Jerkass for demanding compensation for you smashing his bone china vases, but it's really just an example of Reality Ensues in a game where you can smash things without impunity (also, Sue-Belle in the beginning of the game if you smash the pot in her head will be crying when you talk to her and will swipe 10 rupees from your pocket)
In the Second Quest, Link will wear the "Hero's New Clothes", which are nothing and he's seen wearing his blue shirt and orange pants. In the ending FMV, he's seen in the green clothes from the normal quest, which could be a result of animation oversight, but if you take into consideration how the "new clothes" could only be seen by those who truly acknowledge Link as a hero, the player DOES see them at the end after Ganondorf's defeat.
The fact that in this game Link is able to control the wind makes a lot of sense if you remember that his Triforce piece, the Triforce of Courage, is Farore's blessing. Farore is the goddess commonly associated with wind.
The locations of the Triforce Shards are all rather creepy. Seems like coincidence, until you remember Link's piece is the Triforce of COURAGE, so to obtain courage, he needs to go through terrifying locations to prove it.
Every ten floors in the Savage Labyrinth is based off of the enemies in one of the dungeons. First ten being Dragon Roost Cavern, second being the Forbidden Woods, third being the Tower of the Gods, and the fourth being the Earth Temple. Why not the Wind Temple? For one, it introduced no new enemies, and two, you can visit the labyrinth before stepping foot into the Wind Temple.
Why was Gohma attacking Valoo's tail? Well, aside from causing him the discomfort that it did, think about where the other two pearls in the game were originally hidden: in the care of their respective spirits, usually inside something that dangled, and swayed to and fro - for the Great Deku Tree, the pearl was hidden away inside the highest part of his crown, and Jabun's was inside the lantern on his head. Upon closer inspection, Valoo's tail does have similar movement patterns to both of these, thus, it's likely that Din's Pearl was once held in the hook at the end of it, and that Gohma was sent there to get rid of it. If this were the case, it's pretty lucky that Valoo decided to bequeath it to Komali's grandmother as a gift - if he hadn't, and it was still in that room when Gohma took over, Ganondorf would've successfully disposed of one of the three things Link needed to defeat him!
The Legend of Zelda series is heavy with destiny, and Wind Waker subverts this theme at every opportunity. Pretty much every Link prior to Wind Waker were a part of a long chain of ancestors destined to protect Zelda and defeat Ganon. Each of the three primary characters in the series are constantly fulfilling their set roles, but Wind Waker deviates from this path. Link has no relation to the Hero of Time, Tetra has her own identity as a pirate. In fact, it's the characters who break the chain and forge their own paths who make it out well in the end. Even Ganondorf has grown tired of this constant chain, and seems to have matured considerably since the events of Ocarina of Time, but ultimately the instinct to conquer is the only thing he knows and he's powerless to break free from the cycle as Link and Tetra have. Likewise, Ganondorf's foil, Daphnes, must accept that he is holding onto a dead civilization, and if the world is to continue he must let it go. But all of these examples are pretty overt and don't really enter fridge brilliance territory until you consider the fates of Makar and Medli. In Ocarina of Time, Saria's awakening as a sage was bitter sweet because it was like she was losing her identity as Link's best friend. She was something greater, and it was essentially like a life sentence, but she accepted this as her destiny. In the end of game we see that Makar and Medli have left their temples and are free to return to their lives because Ganondorf is forrealz dead and there's basically no reason for the sages to continue doing sagey things. Essentially, Wind Waker chronicles a story of emancipation for all of the people in Hyrule trapped in an endless cycle of fate set for them by the goddesses.
Why does Beedle start selling bombs only after you go through the trouble of stealing them from the pirates? Because Tetra broke up Bomb-Master Cannon's monopoly on Windfall Island.
The Master Sword is completely depowered when Link recovers it. That could mean Fi is actually dead when you first recover the sword!
Most of TWW Link's life. Not only are his parents and grandfather dead, but the very first thing you do in the game is accept your coming-of-age presents. This means Link is the Man of the House atage twelve, possibly younger. And what's the first thing he gets asked to do as the Man of the House? Rescue his sister from a 30-foot man-eating bird. Of all the ways to get thrown into the world, this ranks as one of the worst; his innocence hasn't just been lost, it's been shattered into a thousand pieces.
Medli and Makar on on the Pirate ship greeting you in the final cutscene. But they were required to stay in their temples praying so the Master Sword would retain its power. Did Ganondorf break free because of this? If yes, then he would just have drowned because he no longer had the Triforce of Power to keep him alive. And a huge sword wound in his head.
The beginning of the game: if the pirates hadn't shot down the Helmaroc King, Ganondorf would have gotten his hands on Zelda too soon.
If you watch PBG's G Files episode on Zelda, near the end, he'll talk about Tingle. In his Majora's Mask incarnation, he's just a kind hearted boy who just so happens to be obsessed with fairies and has the mind of a child... But in Wind Waker... Things get scarier... Let me ask you a question... Where do you find the Pictobox? In Tingle's cell. Right! But if Tingle was the one who stole the box, that means he had to have carved that area out... So, what are all of those SKULLS doing there?!? And what about if you visit his island and how Ankle and David Jr. claim that whenever you use the Tingle Tuner, he's nice to them... "So nice!" Have you connected the dots yet? That's right. Not only is the WW incarnation of Tingle a slave driver and abuser, he's also a mass murderer. As if Tingle wasn't weird and/or creepy enough.
In the Earth Temple, you encounter many Redeads. Now the Earth Temple has many tombs in it, and some of the Redeads come out of those. However, others are found sitting in rooms with no tombs. So when the flood came, they must have been attendants trapped within the temple to die a slow death.
There are Redeads in the basement of the teacher's sea cabin.
Ganondorf's motives as revealed in this game are made even more tragic with the release of Skyward Sword, in which the supposed predecessor to his country...is shown to have been the kind of lush, green, fertile landscape that he's always wanted it to be, only to have been reduced to a desert not by any sort of natural causes as one might think, but rather because the selfish members of the ancient civilization that lived there managed to strip it dry and rob it of all its useful resources before leaving what little was left to rust away into a ruinous nothing...Guy's got a bit of a right to be bitter now, doesn't he?
Greatfish Isle. Not only is the sight of the island horrible enough, but it gets worse when you realize that there was evidence of civilization among the ruins. You don't see any new characters appearing on other islands at this point, and there appears to be the wreckage of two canoes lying on Greatfish's shores...