The story is great, but it blatantly gets in the way of the rest of the game

[DPZ2]

thats kinda what i was getting at with you unlocking the previous expansions NG+/ unlocking the next area it jumps your story position to the starting quest of the new expansion so when you skip post ARR and get to ishgard for example you have a new quest in the top left corner that show the first HW quest instead of whatever quest you were on

Um... you know that's what the Story Skip actually does, right?