Bring in factions.

[SannaR]

The most jarring moment of the game clashing with it's own theme for me was in Stormblood.
The MSQ is all about ending the tyranny of unfair governments by helping revolutionary armies. And then there's the lvl 60 to 70 samurai questline where we help the police fight against a man wanting to start a revolution against the clearly corrupt Hingashi government.

Of course there's some differences between the MSQ and the job quests, like the oppressors being the actual government instead of invading forces. Or Ugetsu killing around lords and people getting in his way like the police.

But the thing is, he was justified, the lords killed his family and oppressed the people. Things the garleans did in the MSQ that warranted a revolution.
But instead we work with the police to protect this clearly corrupted government.

It felt so at odds with freeing Doma and Ala Mhigo from their oppressors and then denying the same to Hingashi.
I would rather not have help the government in the first place.

I feel as though that was part of the point of those quests. To make you wonder who's in the right. Neither side is good. It's also a huge nod to what was happening and how people felt and acted around the beginning of the Meji Era of Japan. Where yes there's corrupt officials and there should be a way to deal with said officials, but you also can't have people going around trying to kill or killing people. As that just causes a different set of problems.