I think it just comes down to a lack of consistency. We always knew that Hydaelyn was responsible for the Sundering, which in itself was always an act of genocide. It was just a matter of whether it was an intentional act or an accident - and quite a few of us were more than willing to give her the benefit of the doubt prior to Endwalker. As it happened, not only were her motives exceptionally dubious none of them hold up under even the slightest bit of scrutiny or would be accepted if they were instead aimed at the protagonists of the story. So I never got the impression that the story was ever going to be black or white even when we only knew some vague details.
I know a lot of people who only really started paying attention to the story during Heavensward and again in Shadowbringers due to the nuance that was present. Stories involving straight up 'good guys vs bad guys' only really work if the 'bad guys' are allowed to earn a victory from time to time. Sephiroth and Kefka are so memorable precisely because they 'won' to an extent. Yet the game's increasing aversion to anything resembling meaningful consequences for the main cast ensures that it's often difficult to care about anything that the Scions do. The game likes to not only clad them in ridiculous levels of plot armour but pretend as if their specific point of view is almost always correct.
Many other RPG's have more varied characters with different opinions, personalities, belief systems and goals. They may align with certain interests from time to time but it doesn't stop them from clashing every now and then. FFXIV is in dire need of more than that and although Dawntrail promises to go down that route, I'd be surprised if it didn't result in the Scions all coming to agree by the end of the base MSQ's.
A lot of people were also hoping for a more interesting cause behind the Final Days. Some sort of alien entity along the lines of Lavos, Jenova or Ultima would have been perfect - and arguably a lot more engaging than Meteion. Dynamis was also a rather grotesque element to add into the equation and one I suspect was only conjured up out of nowhere to try and justify Venat's actions as a 'necessity'. It's just a shame that the game spent a decade being exceptionally preachy and screechy only to fail to commit when it mattered most. It basically just revealed that the Scions have no real issue with the things they claim to fiercely oppose so long as the 'correct' targets are being wiped out.