My primary hopes are they quit pushing Venat/Hydaelyn as good and the Ancients as having deserved their fate. I don't expect a rewrite, but characters and text in the game (as well as the short stories I'm apprehensive about) can at least stop referring to that tragedy as a positive thing (or ideally even a reasonable course of action). ShB was much more nuanced. The journal entry for the Shadowbringers quest reads: "You wage a titanic battle not only against Hades, but the hopes and dreams of Ascian-kind, of which he is the keeper. In the end, however, your own unwavering conviction brings the ancient being low. You have done a great and terrible thing."
Plus there's Pandemonium, which has been another source of concern because the dialog with Themis seems to suggest that Azem knows about sundered self and that is definitely crossing a line for me. I suspect Yoshi-P thought everyone would love Venat and the idea of working with her and... no. I'm frustrated, to say the least, that after the neutral Azem we were presented with in ShB who chose neither side that there are some implications we did side with her after all (not to mention us outright siding with her in EW despite the fact that Hydaelyn represents everything the WoL and the Scions have historically been opposed to).
I'm going to state this in bold print: Azem working with Venat is so inconsistent with everything we know of the Azem soul that I would consider it a character and game breaking retcon.
Anyone who feels differently, I invite to replay through the game. I have been on an alt. Pay particularly close attention to the dialog surrounding the WoL, such as Thancred saying they fight for friends not nations, and basically Ardbert's entire arc in HW. Azem siding with Venat means the betrayal of everyone they love and it just wouldn't happen.
I get the impression after EW that Yoshi-P's vision of the WoL is a traveling murder hobo and I think the character and the story has been undermined as a result.