An easy fix for the cutscene exploit would be to make it so whenever you start a cutscene in those dungeons, you get a debuff that immobilizes you, locks down all your attacks and abilities, and makes you invincible and invisible. This debuff would last for the full duration of the cutscene, so if watch the full cutscene, the debuff will expire at about the same time the cutscene ends. If you exploit to skip it, congratulations, you get to stare at a debuff for 5 minutes or however long the cutscene is.