Things Hyao could change that could improve the smothness of the story events, in my opinion, is NOT letting the player decide if you are going to save Bernard or Logan during the attack in Bareshade.
I thought about it while solving (or trying to solve) a topic with one of the users here exactly about it.
In my opinion, if you do not encouraged Logan to go to the Bandit's, the MC should totally look for him without thinking since we hear an howling coming from the Sawmill. Whatever is happening with Bernard could wait, would make absolute no sense to let the city in danger to save Bernard.
Logan matches a way more with the Full Moon plotline than Bernard. He has all the reasons and the character development to this situation.
Saving Bernie would just be a "choice" (since you would have no other option) if you encouraged Logan and got the Bottom Logan route.
I know we would lose some contents, but, on my opinion, it would match the story so much better in this way.