- Widescreen 1080p with complete re-rendered/drawn textures, a brand new lighting engine, and a variety of new graphical effects
- Redone music, emphasis on still sounding like "Wind Waker" while improving samples and incorporating new elements
- Select "hero mode" at any time on file select to double enemy damage and remove recovery hearts
- Five of the eight Triforce pieces are now found in the chests that used to contain maps to their sunken locations, eliminating the need to acquire 1990 rupees to decipher the charts
- The Wind Waker can be conducted via the GamePad touchscreen, and the second playthrough of a song you conduct has been removed, speeding up the process of conducting any song
- After playing the Wind's Requiem in your boat, the camera pans behind Link, and points in the direction you want the wind to go, instead of panning above him with an arrow
- You can acquire the "Swift Sail" relatively early on in the game, which doubles the speed the King of Red Lions sails when you press the A button (this only works because the entire ocean is now loaded in RAM at once, so there is no need to sail slow while loading new areas)
- Improved draw distance on the Great Sea
- The Wind Waker, boat cannon, and boat grapple for pulling up treasure are all mapped to directions on the d-pad, so they no longer require equipping and the taking up of button-inventory space. You also no longer need to equip the sail, it is mapped to the A button when you are in the boat.
- When aiming the cannon in the boat, you now have an aiming reticule
- The clouds over the great sea have been completely redesigned in a more lush and realistic style, while remaining fully weather-dynamic
- You can walk while in first-person, and walk while aiming items like the bow and arrow
- You can aim your first-person items using the GamePad gyroscope, like in OOT3D (useful for fine tweaking once you use the stick to put the cursor in the general place you want it)
- The pictobox now holds up to 12 photos, increased from 3
- The pictobox displays a "Great!" emblem when you successfully take a picture of a character to have a figure made, so you know if your photo was good enough without having to take it to the guy first
- You can use the pictobox to take "selfies," where Link holds the camera towards himself to take a photo of himself and what's behind him
- The touchscreen inventory on the GamePad allows for easier assigning of items to buttons
- You can find bottles on the beach that contain messages from other Wind Waker players via Miiverse, and put your own messages in the sea the same way
- When sailing, you can have the map on the GamePad screen, making it much easier to position your boat when looking for treasure. The treasure map you have will display smaller next to your main map, so you can place your boat in the correct place. You used to have to keep pulling the map up over and over, often overshooting your point.
- When you start the game, your wallet's maximum capacity is 500 rupees, rather than 200
- Grappling hook animation cut down to less than half of its previous duration, both on land and when dredging up treasure in your boat
- Sped up text boxes, and removed repetitive explanation for how to equip new items
- Option to play the entire game off-TV on the GamePad
- I bet I'm forgetting some stuff I'll be annoyed about later
