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Wind Waker HD and Ocarina 3D have about the same amount of gameplay changes and improvements on a similar level, don't kid yourselves. It's not like they included the water dungeon that was cut from WWHD, so you can't fault OoT3D for not including the light/wind dungeon either.

Looking at the game, it's no contest; Ocarina of Time wins. But I guess we must ignore that and only look at the remakes and what they brought.

Ocarina 3D included Master Quest and the Boss Battle mode. Wind Waker HD, while making the game a lot better in my opinion, included only the Hero Mode. Which is the same as the vanilla game but more difficult and without the hearts. Master Quest on the other hand is more difficult (even more difficult relatively than WWHD's Hero Mode I might add), but also rearranges every dungeon while it's at it and mirrors the whole world including interior spaces. It's basically a second game.

Winner: Ocarina of Time 3D.