First, Bakuul Ja Ja, he was first introduced a big evil rival who's going to try to mess with the others and cheat his way through... But then they explore his backstory, and he's actually has a good bit of depth to him... But then they just drop him from the story and consider him redeemed after 2 cutscenes.
If they wanted a good story, he should have come with us to Alexandria and have his redemption arc there.
And moving onto Alexandria itself, most of the story with it was pretty good, except for Sphene... Sphene kind of can't decide if she's supposed to be a sentient person, or a machine wanting to harvest souls to maintain the Endless' power supply.
And when talking with her about Alexandria's past, the WoL kind of just stands there quietly when (s)he could just fill in a lot of blanks to the story, like the Flood of Lightning... And when talking about the extra Lightning aether causing paralysis, that they'd very likely have somewhat of a cure for it...
And then in Living Memory, the first two areas out of the four are kind of just padding, they don't really add anything to the story and they could have spent that extra time on Krile's parents and Cahciua...