Angler's Tunnel and Catfish's Maw, as well the Marin quest and Ghost quest. Also, Link and Marin's understated romance, not playing the Color Dungeon, and of course, more discourse on how the dungeon maps look like things.

The Bottle Grotto and Key Cavern dungeons, as well as their interstitial quests (rescuing BowWow and retrieving the five Golden Leaves).  Also, Jay gives a math lecture, reprising the topic of Link's left-handedness, and the use of dogs in Breath of the Wild.