Namely, loose threads and buildup without the climax.
Dlc3 tried to do a big buildup to reveal that The Company was Jakobs. Although it was kind of easy to predict, it still is an interesting idea worth exploring; were they experimenting off-world? Were they on Gehenna originally, and moved to Eden 6? How involved was the Jakobs family, and how would Wainright react to what his corporation had done?
Problem is, after that Jakobs logo appears in the elevator, it’s not touched on again. Just the dramatic reveal (which, again, you could pretty much guess ahead of time) without delving into the implications or explanation.
Additionally, Rose seems interesting, but we don’t understand her motivations, and we only get a glimpse at her backstory through an echo or two. Given what she knows and how much of an impact she makes, why aren’t we told what changed her from daughter of a scientist to psuedo-revolutionary anarchist gangster?
I’ve found these problems in the main story, as well, specifically in regards to two things; Troy’s tall puppy syndrome, and whatever the hell Lilith did in the end credits.
The Lilith problem is simple; the game acts like it’s obvious, but it really explains nothing. Did she turn into a fire hawk logo shaped barrier? Is everyone on the moon dead?
As for Troy, they really built that one up quite well. He surprised everyone by taking Maya’s power and life, proving that he is more than just a ‘leech’, and immediately it starts going to his head. Soon he is competing with and challenging Tyrene while working with her, and it makes the dynamic much more interesting.
It even escalates back on Pandora, when you raid the cathedral; he is getting impatient and angry, even abusive, because he feels oh so important and above everyone, he even risks hurting Tyrene to get the job done, ignoring her hilarious screams in his boss fight.
But then, he just dies and Tyrene eats him. That is not a problem, but if it’s going to play out the same as if he had never changed character, why bother with all the drama? No climax, despite almost a 3rd of the game building up to it with all this tension between them from him gradually becoming more and more self-important.
All they had to do was throw in a line, like “you’ve forgotten who the real star is”, or “enough!”, and it would have gotten the point across, but Tyrene shows almost no I’ll feelings about it before absorbing him.