I could've suspended disbelief for most of it, but not:
1) The Scions' admiration of Hydaelyn despite her being an amalgamation of antagonistic ideologies they have historically opposed. They do unfortunately have a history of zealotry towards her dating back to ARR. However, Krile goes from supposedly being skeptical of Hydaelyn's nature and motivations to embracing her wholeheartedly because she was just too charming to resist (and the game does not attribute this to tempering). Not a single Scion gives a sanctimonious speech about how wrong her methods were or the fact that they're benefactors in a literal crime against humanity. Nor do they address the deeper implications of that given they're supposed to be our moral paragons in the game.
2) The conflict between the presentation of Hermes (villain) and Venat (heroine) despite not only their motives (dissatisfaction with Ancient society) and results (end of Ancient civilization) being similar. Why is one bad and one good? Yoshi-P even compares Venat to the Ascians and, again, I'm left wondering why she's not also bad when she's guilty for as much and more while having less sympathetic intent.
3) The reasons for the sundering as a whole were not sufficient. Quoting Lurina from the lore forum: "The more controversial a plot element, the tighter the plot has to be to get people to accept it in good faith, and 'cultural genocide was the right call to save the world' is about as close to maximum controversy as you can get. I think the fact that these forums, the comments on Venat's entry in the JP character poll, and pretty much everywhere else the story is being discussed are filled with people expressing discomfort or irritation with it self-evident proof that the writers didn't quite make it."
4) Nobody being angry with Venat after the fact. The WoL clearly cared about Emet and Hyth, they trusted Venat to do the right thing, and she arguably didn't (don't @ me with tImE lOoP). The WoL nevertheless is "fond" of her. Emet, who is everywhere presented as having suffered through 12k years of "hatred and heartbreak", waffles between taking digs at her (I only accept the reason he wasn't furious is because he'd either already gotten it out of his system or, like Brinne said, didn't want to upset the WoL) and commending her, which was so inconsistent with his character it wasn't believable. We got more bitterness out of Elidibus, who died never learning the truth.
I'm sure I'm forgetting some things that may come to me after I post this. :P