One tiny thing that might help in your analysis: Nintendo accidentally included all the symbol names and locations on the Wind Waker disc in a file called "framework.map".
Doing some basic demangling on the CodeWarriors names gives you C++ classes and methods:
The "sea" animation is controlled by "daSea" -- "da" meaning "dynamic actor" in Nintendo's naming terminology.
It's extremely unlikely they used texture distortion for the sea effect, since the GPU they used didn't have fragment shaders -- the only method of texture warping is INDTEXMTX, which was only used for the heat effects in Dragon Roost Cavern.
They probably modified UVs directly on their triangular sea mesh.
Smoke effects and such use their in-house particle engine, "JPA".
At my old company I wrote an assembler to read text source and assemble the instructions into TEV format.
My point was more that TEVs can't modify texture coordinates, since texcoordgen happens before the TEV stage. TEVs only specify how to blend vertex colors, texture samples, game-set registers and lighting results together using configurable formulas.
> the only method of texture warping is INDTEXMTX, which was only used for the heat effects in Dragon Roost Cavern
Remember that as far as the major releases go it was released in 2002 after Ocarina of Time in 1998 (and a sequel using the same engine in 2000).
People wanted a "real" Zelda game with "real" graphics, like what became Twilight Princess in 2006, whose graphics are a logical follow-up to Ocarina of Time.
It's funny how history turns out, now Wind Waker is widely lauded for its graphics, and it looks much better than the likes of Ocarina of Time or Twilight Princess.
It's a fantastic example of how Nintendo is still a company that dares to experiment, even with their most wildly successful game franchises. That hasn't always worked out, but we've gotten amazing innovative games like Wind Waker as a result.
There are also some epic design failures: the biggest one, to me, is that the games give you the boat before it's ready to let you explore. Instead it walls off big chunks of the world to railroad you into going to Dragon Roost Mountain. As soon as I got the boat, of course, I headed straight for the nearest island to see what was there, hit a wall and was turned back. I found that showing me the open world and then not preventing me from going there, and in such a clumsy manner, was very disappointing. I think they'd have done better to have simply moved you to the island outside your control, and only let you take command of the boat once you pick up the baton.
A lot of what gives the game its character was the seamless loading between islands. Twighlight Princess, which was a perfectly decent game, seemed much smaller to me because of the endless constrained environments and loading screens.
Meanwhile, I still haven't finished Skyward Sword.
What continuity is there in WW? Nothing jumps to mind, especially when the previous game (Majora's Mask) was essentially a direct sequel to OOT in comparison.
The main character is dressed as Link because children dress as the great hero once a year.
People thought that this would be the next Zelda game.
Nintendo are at their best when they're unconstrained.
I say 'one of' but I can't actually think of anything better at the moment.
But it's also my favorite when it comes to gameplay and audio. I don't think I've played a platformer all the way through as often as I've played through Yoshi's Island, and its music still randomly pops into my head quite regularly.
Here with some animated gifs: http://kemenaran.winosx.com/posts/links-awakening-rendering-... (disclaimer: I'm the author).
Edit: after reading said post, it's a great explanation of the techniques used in Link's Awakening's intro. That game looked gorgeous on the B/W Gameboy, it's cool to actually understand how they managed to pull it out technically.
In particular, skip ahead to 33:54 to start with the "Dawn" fanfare followed by Wind Waker's fantastic Ocean sailing song.
GTA V - Graphics Study
If the designers had followed the trend at the time and gone for "realistic" 3d with textures it would look horribly dated now.
But they did the right thing and it has aged extremely well. And the re-release looks great on the Wii U.