I think I worded this lazily, hmmm, I'll try again.
Agreed that many of the people of Elpis felt more human to me than the people of Eorzea. I was sure I wasn't going to meet any Lominsan sex slavers there, that's for certain. I think that the writers tried to make the Ancients seem much more flawed than they were through the MSQ. By implying that no one was willing to let Hermes be sad or even that having to put down arcane entities was somehow inhumane, thus attempting to show that they had no empathy. And a lot of people bought into it. I see these being parroted as prime examples of why their society was doomed to failure all the time. Because using a butterfly to make a robe is heinous even though almost everyone has worn leather and animal products at some point in their lives (and arcane entities are just aether), and destroying rabid arcane entities is "having no respect for any life other than human". They were content as a people, yes, and there is absolutely nothing wrong with that. The Elpis flowers always being white is not a bad thing, but somehow the MSQ tries to make you feel as though this is an aberration. It subtly pushes the idea that everyone not being sad or in a state of constant emotional flux is unnatural. That the Elpis flower not changing colors 150 times a day means that no one has feelings except for Hermes, that they were just robots.
Meanwhile, in doing the side quests you find that there were other people who felt complex feelings (even sadness!) for their creations and no doubt would have shared all of this with Hermes had Hermes actually tried stepping out of his own head and talking to the people around him once in a while. The side quests also show you that the Ancients, while structured, were also open to new ideas and to implementing changes when they saw the merit in a new idea. No one was stopping anyone from having negative feelings, they just didn't seem to have a system in place the way we would for expressing and working through those feelings when they did have them. But there also isn't any reason to believe that they wouldn't have been open to exploring new ways of helping with that either.
This is more what I mean when I say there is a disconnect. the funeral quest alone made me tear up because I was happy to have been able to share something new with them and see how excited they were to use it in the future, only to remember that these people would be killed soon, there was no future. While the MSQ wants me to believe that because Elpis is "paradise" that it must have a seedy, putrid underbelly and all of the Ancients' society is headed for self-destruction because they are too content and unwilling/unable to change.