What they could, and probably should do, is streamlining the MSQ.
You can tell it was a distraction put in like this in ARR, to buy time.
Cut out the fed-ex stuff, let the story develop at the same pace it did up to 50 and add appropriate XP.

Spending the same time to get 4800xp out of the mandatory MSQ while i get the same for 3(!) mobs in a dungeon feels like punishment.

I'd not change the fact the quest have to be done, or the inner logic of char progression will collapse.

Being promoted to ninja only to have them enter the world at a much later point would make Yugiri and her story not only pointless. Players would feel like SE made fun of them.