There are some things, that don't really add up or just make me wonder a bit
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Gortash and plot reveal
If you don't go through the game blindly, you find a lot of notes between Ketheric and Gortash in Moonrise Tower, detailing their whole plan with the Elder Brain. So why do our characters make surprised Pikachu faces, when he and the plan of the three Stooges is revealed at the end of act 2? I was also a bit sad, that Karlach had nothing to say to those letters concerning Gortash and his involvment. I know, she and Wyll got pretty much sidelined, but still, at least the last scene should play out differently, if you find the letters and already know everything. I think, even Orin isn't a surprise, if you save Minthara in Moonrise, since she tells you about her recruitment, if I remember correctly.
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It's similar to the situation with Shadowheart and the Dark Justiciars. In Grymforge there are dead DJ's everywhere, their statues and armour, documents and letters. And this prompts comments like "I wonder if this is related to dark justiciars" and '"we must keep looking out for traces".
After talking to Raphaël in Shares' caress where he bluntly reveals why he wants the crown of Karsus, I would normally have had a word with Mizora in our camp and tell her all. So she could help us into hell and steal that Orphic hammer. Unfortunately we don't have that option.
I also find it strange that no one takes a clue from the steel watcher's comments on Karlach's heart. If the Gondians can make a stable version with better material and advanced technology, then the ironhand gnomes should also be able to do that also. The logical ending for Karlach, IMO, would be then to let her take refuge in the House of Hope, while we get either the Gondians or Wulbren to create a new heart for her that is stable in the material plane.
