Let's expand ghost ships to just saying that any moment in an RPG that has you stuck on a boat sucks (IoG's mayan gold ship is a notable exception but then it has the raft bit so...).
Legend of Mana: The gameplay.
The thread's about annoying /moments/ in games. If we just awkwardly were picking RPGs that had broken gameplay we could just be all "90% of everything" and that'd be the end of it.
re: Dice wrt LoM story:
Some stuff in the story is intentionally left open to interpretation, and some of it's because there was some cut content, but really most of the gaps in the story come from huge swaths of it being optional (notably, you can miss most of the World History encyclopedias, and you only need to do like 25% of the quests to finish the game).
I don't think anything in the game or the Ultimania actually explains what the Lord of Jewels is, though.
The customization not being useful in LoM is the biggest part of the gameplay that bugs me. The combat being easy on its own is like, okay, whatever, not a big deal. It's still fairly fun just to wail on baddies and unless you're on hard mode it's not obnoxious. But the easiness renders all the optional gameplay kind of useless. Monster collecting and building golems is nice enough on its own, but the crafting systems don't end up serving any purpose, and there were also glitches with the monster personalities being imparted from food, iirc.