Even Zenos's revival... they ruled out any redemption arc from the outset. Still, he has a lot of fans, so I'm not sure how successful their attempt was.
There was Yotsuyu. They amply expanded on her backstory and how it tied into how she was treated as a Doman. But you're right, a lot of this stuff is tied into side-quests, and that was the exception. There's certainly a lot of material that highlights that the average Garlean, whilst misguided/misled, is not necessarily evil (and conversely, that Eorzea/Othard has its own share of wickedness.)
Even in Nidhogg's case, whilst his rage was explained to us, he was so uncompromisingly destructive at the end, that nothing but death could resolve that story arc. Which, in turn, explained Thordan's motivations.