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Knuckle is required to complete Figurine Gallery and get Link and the King of Red Lions. Hero's Charm has been moved to the bottom of the Savage Labyrinth, with that Piece of Heart now the treasure in the Two-Eye Reef.
There are now new Treasure Charts, replacing the ones from the old Triforce quest, gotten from 1) Giving Miss Marie 40 Joy Pendants (used to be Hero's Charm) 2) Platform at Horseshoe Island 3) Platform at Star-belt Archipelago 4) Pig mini-game at Windfall Island 5) From one of the secret cages on Pawprint Island.
Also, the Magic Armor now consumes Rupees, not magic. Which I don't like.
There are definitely more changes, but these are the ones anyone going for completeness needs to know.
Thanks. I actually like the Magic Armor in WWHD. It's more useful (mainly on Hero Mode). It's what TP's Magic Armor should've been, you'd only lose rupees from getting hit not continually.
Official Guardian Knight Slacker of Safe Haven. Light blinds us and forces us to stumble about in ignorance - Altair
Magic armor is way more useful now, and gives all the rupees in the game a much larger purpose now beyond the stupid triforce quest. It's certainly a positive change, and it can last a lot longer than it used to.
The only negative change I'd say the game has is the little mask to see enemy HP being so late game now. In some ways it's better, because it makes the second half of the salvage lab more worth it. But it's a shame we can't get it as early as we used to. At least it doesn't require grinding anymore, though. I think most people would get it late game anyway because it'll take a while to get that many joy pendants unless you grind for it.