I think I finally figured out what puts me off about the XII story. And I don't think I'm the only one. I see a lot of people playing the game excited then having their enthusiasm deflated around the time they get to Mosphoran Highwaste.
The Highwaste mission is right after what was unforgivable to me, ruining all claims of "realism" of the story: Attack on a refugee camp (Mt. Bur Omisace) and murder of a religious figure treated as "business as usual" not only by the bad guys but by our own party!!!. Sure X had the destruction of Kilika but at least there's a tiny scene / plot where Wakka and the others are helping reconstruct the village and Yuna is bringing comfort to the dead. In XII it's like "oh, Anastasis and the refugees died to buy me time to get the sword ? Great job, see ya later suckers!"
I don't want to spoil it but there is only one single scene where someone from the outside tries to help the survivors, we actually only see a single Viera worried about them on the Fafnir hunt.
In real life, even one as smurfed up as ours, the bombing of a refugee camp and the murder of someone as high as Anastasis (the pope ?) would have been a big scandal and there surely would be people helping out. Neither one of our 3 "good royals" cared enough to do so. The game ends and there still no mention of Rozarria, Archades or Dalmasca helping the survivors.
And Anastasis isn't the only one that gives his life to help our party and gets a "see ya later" for his troubled community in return (SPOILER)Reddas dies and no one in our party goes to help his friends keep Balfonheim port as he had it, which means it will probably going to fall in the hands of Reddas haters
All in all, it is full of examples of people giving their blood, sweat and tears to the royals in the hope that the prince or princess might be good people and rule wisely. A very servile / peasant POV the I hate. Serfdom has already caused enough trouble and injustice in real life.
The morality of XII is seriously flawed IMHO, which wasn't the case in previous FFs.