I'm playing the game right now (no, I don't mind the 3D remake, because I don't have a 3DS), and got to that Beneath the Well mini-dungeon. The one where the Gibdos ask for items, you know? Well, every single hint was pretty intuitive, and anybody with braincells could realize what they were.
Then I hit a "deliciously fresh" description. That's rather vague to begin with. I gave up, looked at a guide and... it's a fish?
I wasn't even aware you could catch a fish on a bottle, but how am I supposed to associate "DELICIOUSLY FRESH" with a LIVING FISH ON A BOTTLE? Oh, it says those exact words on the description after you catch him. Well, too bad I never had to ever catch fish in this game before. Not to mention, fishes are completely useless other than progressing this specific part of the story, so I have no reason to EVER catch them.
So far, I don't think Majora's Mask is too guilty of being overly cryptic, once you realize the game expects you to talk to everyone and pay a little more attention to detail (though there can STILL be some bullshit), but this... this is just bad design. I hope they tweak this sort of shit on the remake.