While it could simply be the complaints of the disenfranchised, I've tried to adjust my perception to account for who we're listening to and how they ended up where they did. For one, it's unfair to assume that everyone just trying to live their lives within a given nation shares the goals, morals, and beliefs of their government (or even one another). We're also hearing these complaints mainly from patriots who fled Ala Mhigo rather than be executed specifically because they rejected Garlean rule outright. The resistance has had its fair share of victories and defeats (though, victories have won them little and defeats have cost them much).
There may have been some public dissent to the attempted expansion into Gridanian territory (though, as far as we know, plenty of people thought the economic growth and glory of conquest were great). King Theodoric wasn't very popular after some of his later decisions, given how easily Gaius van Baelsar's spies turned the people against him. Talk to Erik about that one; the guy was a tyrant. His actions and policies led him to be called the King of Ruin, after all. I'm sure if Ala Mhigo had Gallup Poll records, we'd see the kind of diversity you're looking for.
The Garleans continue to exist in a sort of philosophical gray, whereby they're correct about the threats to the planet and the need to solve them, at least. They didn't do much to give Varis the benefit of any doubts, morally, though, did they... The end justifies the means might as well be the current Garlean motto with his complete lack of sympathy or consideration for the "eradication of certain elements" that might occur.
But, with 3.0, even Thordan wasn't as unilaterally wrong / "bad" as I expected him to be. Given the position he was in with the information he had, I can see things from his point of view (and also, from mine, where he was wrong). I was pleasantly surprised, and if they can even give "Jeuno with a Pope" some redeeming qualities, I assume we'll continue to see some from Garlemald. Maybe not from Varis...
But was Gaius so wrong, in the end? And I'm talking about 1562 Gaius, before the whole downward spiral through Silvertear Skies, Nael van Darnus, dying Emperor, and Ascian Puppet. The tempered do need to be put down until such a time that we can find a cure - Thancred admitted as much. The primals do need to be eradicated. Our world is at stake. The guy's downfall was that the Empire is wholly unwilling to compromise and assumes its logic is infallible. That is the part I'm not sure if we'll see change at the faction identity level. "Kill them all and let (their false) gods sort them out" is kind of hard to humanize aside from having interesting and dynamic individuals who are handling that approach in different ways (with regards to the leadership/military), or who are dealing with the position that puts them in (with regards to everyone else in their territories).
Personally, I hope we meet a lot more Garleans like Rhitatyn sas Arvina. Despite his small role in the game, he was one of my favorites. Go back and watch those Westwind cutscenes and compare his sentiments to Urianger's lamentations that "doing the right thing" makes the salvation of this world so much harder, and take so much longer, and demand so much more suffering and sacrifice, but is just something we have no choice but to bear. Do you risk failing to save your world by refusing to become a world not worth saving, or do you do whatever it takes and worry about redemption after you have results?
We do need antagonists that aren't Ascians, though, so don't be too disappointed if you still hate them even if you can understand them, lol.