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I played through both OoT and MM and now I’m reading the manga adaptations of each. They aren’t super long so each dungeon only gets like a chapter, but there are a couple changes that I like. For instance, there’s more interaction between Link and the Skull Kid who would end up with Majora’s Mask. Also, Link doesn’t just forget about Saria’s Ocarina when he gets the Ocarina of Time, rather he drops it when Ganondorf attacks him and Ganondorf takes it from him thinking that it’s the Ocarina of Time.
He also meets a cute bird boy that doesn’t exist in the game.