In Ul'dah the Thorn Dynesty enslaved and then sealed an entire race of Beastmen underground. One of the main reasons we have to fight them now is because of what the Ul'dah people did to those Giants in the first place.
Ul'dah turned Sil'dih's population into zombies with an alchemical weapon. In Ishgard, the first DRK became a DRK because he caught a clergy member raping children from the Brume and when it was brought before the Holy See the would be DRK was condemned for killing a clergy member.
One of the characters in the DRK story had his entire tribe of Au Ra refugees attacked and slaughtered by Ishgardian soldiers because they had horns and scales. These same soldiers had previously attacked the Au Ra and been spared.
The Kobalds are summoning Titan because the Limsans chose to break their truce with the Beast tribe to take land by force. Now the Kobalds understandably don't trust Limsa with any type of treaty.
The Limsa is still full of pirates. Its just they only attack Garleans. There is however no laws on how they treat Garlean people they capture.
There is a reference in one quest that suggests young women still are at risk of getting snatched of the streets of Limsa and end up on brothel ships.
There is a quest in Gridania for the Beast Moogle quests where a group of Woodwailers almost rape a pair of Seekers of the Moon because they are 'suspicious' which ends up forcing one of the Seekers to go back to live among the Seeker bandits. There are likewise a couple of times Duskwights are treated as untrustworthy and traitorous simply because of their race.
On the Garlean side of things, Garlean's obsession with conquest as well as their treatment of the conquered is horrible. That said, as screwed up as it all is, people who serve Garlemald, even as conscripts, earn citizenship along with all the rights and advantages that holds. I would also argue we haven't seen any potential benefits that might have helped conquered societies such as civil security, standardised trade, improved infrastructure and improvements in things like medicine.
None of that washes away the bad things Garlemald has done and it doesn't change the fact that the Military allows these types of things to happen. However it doesn't neccesarily mean the nation as a whole is completely unethical, or irredeemable. There were a lot of people who felt Ishgard was pretty irredeemable leading up to HW.
The thing with this is Garlemald is a nation, not a single person. You'll probably be happy to know they have said Zenos is someone no one is likely to sympathise with, indicating he will probably be a complete bastard. However a nation or race should be multifaceted and complex. Nations are. Even in WW2, its not like all Germans were evil people and Garlemald is more like ancient Rome than the Third Reich.