Story skip

[Niwashi]

This list of dungeons includes information on which quests unlock them. Next to the name of the unlock quest is its icon, which indicates whether it's a main scenario quest (flaming circle icon) or a sidequest ("Q" shaped icon).

The story skip unlocks the ones normally unlocked by the main scenario (I'm pretty sure of this part), but I don't think it unlocks any of the optional ones you get from sidequests (I'm less sure of this part, can someone confirm?).

There's also a list of feature unlocks that include both the dungeons and other features. I'm not sure how many of the other features get unlocked by the story skip, but at least having a list of what unlockable features are available will let you check what you do and don't have, and find how to unlock any that you're missing.