Well if we're criticising the case I think the way Dhurke is handled is its biggest fatal flaw
His sins are way too easily forgiven by the main cast. He obsessed over his snail-paced "peaceful revolution" so long that he literally only bothered to visit Apollo AFTER HE WAS DEAD, and that whole trip itself was only done to further Dhurke's goals in regards to the artifact, Apollo became his glorified pawn.
One of the big moments facilitating Apollo accepting Dhurke again is Dhurke saving him from the rising waters in the old ruins. However, Dhurke is already the reason that Apollo was in that situation in the first place, and Dhurke apparently never even bothered to teach Apollo how to swim while he was always playing by water rapids with Nahyuta. This pseudo-heroism and "self-endangerment" that's likely supposed to endear Dhurke to the player flops harder we learn that Dhurke was literally already dead; the person in real danger was Maya.
Dhurke then willfully misleads Apollo by not making it clear that Dhurke is being channeled, and puts his distrusting wife's secrets ahead of the things Apollo needs to understand in order for his own son not to be excuted, as well as Phoenix. It all feels like he just values his adopted son less than the rest of his family, and for Apollo to lap that up in the game is an abominable message.
Somehow, those above actions are supposed to make up for Dhurke's older sins of lying to Apollo, dumping him in America in some orphanage, and never making any attempts to even contact him by proxy or writing, despite him having a legitunderground army of paratroopers, spies, and Japanifornian contacts. Come on.
It wouldn't be so bad if it was somehow brought up how Dhurke had done some extremely questionable things in any capacity, but instead the main cast end up revering him like a saint of justice. A big reason Apollo stays in Khura'in is to carry on the law office like Dhurke wanted. And the subplot of the relationship between Rayfa and Inga and the extent that Inga loved her is completely dropped so that Rayfa can instead sing Dhurke's praise. That in particular left a bad taste in my mouth, when I noticed that it was like I could see the strings of the puppets.
Also Nahyuta is just a dick, he's forced to play baddie in Case 5 but that doesn't change the fact that he and Rayfa were pretty much gleeful over the thought of you and Maya and being hanged. The most annoying was in Case 4 where of course he's as usual a huge dick and tries to physically hurt you for protecting someone's life etc, at least Blackquill shuts him down which is great, but at the end the game acts like you should be happy you "earned his respect" or something. No, he's just a dick, why would you even want his respect? The game made a Franziska and acted like he's a Shi-Long. ---
