The attempted justification of the genocide inflicted upon the Ancients is most certainly this game's 'Burning of Teldrassil' moment. I'm not convinced that the game's story will ever be able to come back from that, since much like how World of Warcraft decided to compromise so many characters and organisations within its story in order to prop up Sylvanas, FFXIV takes a similarly contrived route to do the same thing with Venat. The only difference is that unlike with Sylvanas, Venat was actually killed off. I suppose it remains to be seen as to whether or not that sticks given the game's habit of just casually bringing back dead characters on a whim.

The strange glorification of 'suffering' is also pretty bizarre. Especially when the protagonists are clad in such heavy plot armour that they never go through even ten percent of what the antagonists are forced to endure.