I'm surprised no one has brought up this:
Yugiri is Au'ra. The Au'ra are half dragon, half human... presumably the descendants of Saint Shiva (and perhaps her followers?) who is labeled as a heretic for having laid with one.
If the Au'ra are a new playable race... obviously we are taking their side.
Obviously, we will NOT be on the Ascian side... which means we will be going against the ruling party of Ishgard, who are controlled by the Ascians or in league with them at least.

I'm sure most of the scions would agree not to side with Ascians once that involvement is made clear. Which likely means those who are loyal to us: House Fortempts(? Dragonhead) and the one in Whitebrim will likely try to overthrow the order being controlled by the Ascians leading in a sort of civil war or perhaps a three way war with the civil war and the dragons forming a third faction.
The question will be when does our character learn of the Ascian influence over Ishgard. We already know the Crystal Braves has some "weak links" that need to be checked out.