Bring in factions.

[Cleretic]

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.

A quiet undercurrent of FFXIV's general anti-authoritarianism and pro revolution context is the important underlining of 'while overthrowing a terrible regime is good, you can't do it without a good plan and alternative'. Perhaps most famously, Nanamo's plan to restructure Ul'Dah goes extremely poorly, but it's something that comes up several other times.

• Ishgard didn't exactly pass between governments peacefully, and while it lucked out in circumstances and by having someone like Aymeric to take the helm, it still needed to do complex compromises to get through it all, and multiple side storylines show that even afterwards it still had people who disagreed with it and people who were unjustly screwed over by it.
• Ala Mhigo both has the backstory of their revolution being agitated for by the Garleans solely so they could invade after, and the 4.x story of them trying to find a more equitable government form because all their previous ones sucked.
• While Doma did have the strength of a desired form to return to since nobody disliked Kaien's rule, there is definite understanding that even that still needed to improve.
• The Bozjan resistance didn't just need to legitimize their cause through Gunnhildr's Blades, it also had to grapple with the fact that the IVth Legion was actually better than their previous government for a lot of people.
• And Ugetsu in the Samurai questline is trying to bring back the Age of Blood that Hingans know was a terrible part of their history, and only wants to do that because he himself would benefit from that. He's essentially a bad-faith revolutionary. (By the way, Hingashi's social policies suggest they're actually in a slightly sanitized Tokugawa period, and the Age of Blood is Japan's Warring States period, so Ugetsu's plan is basically 'let's go from bad to worse'.)

Yeah, FFXIV agrees that overthrowing terrible regimes is good, and that's pretty much most of the story both around the Garlean Empire, and of Garlemald itself, as well as plenty of other examples around the place. But it's also aware that overthrowing the terrible regime is just one step of the process; not only can you not just skip to that step, you also can't just call it a day after overthrowing the government... both of which Ugetsu wanted to do.

Basically, the problem with Ugetsu was that he was a selfish bastard with a bad plan. He's an even worse version of Ilberd; at least Ilberd genuinely thought his plan would help people outside himself.

EDIT: Also, while the game never brings it up, Ala Mhigo's probably a cautionary tale for Hingashi as well; at the time they were right next to Garlean territories, who had already taken advantage of neighboring revolutions before. And you can't tell me that Zenos of all people wouldn't have relished conquering Samurai Central.