Majora's Mask nails the intangibles. I love the atmosphere, the characters, the music, the sidequests, and just the overall feel of the game. It falters on the core level design. There's only four dungeons, and I don't much care for three of them. I also find many of the between-dungeon areas to be unspectacular, especially almost everything in Great Bay. Skyward Sword doesn't have music and side quests on par with MM, but imo, it surpasses it easily in terms of level design, both in the dungeons and outside.
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