If I had one complaint, it would be that the MC seems a little too predisposed to bullying Mina rather than having the option to treat her as an equal.
I think you pointed out an interesting point, taught to be good / inherited to be good. MC, in my point of view, is an example of "taught to be good". No matter which background you chose for the MC (voyeur, firestarter or slippery hand), introducing such a background at the beginning of the story did convince me that MC prolly is a natural-born troublemaker (in a general sense) by emphasizing this as one of the three important background pieces out of MC's 20 years of history. Plus the monologue right at the very beginning of the game of how MC trying to convince himself that he is "decent" by pointing out he is a pre-med student, calling mom twice a week etc. It really put a "huh" regarding MC's true nature.
Although it pains me a little of how Mira is being handled by MC in the sex scene, it is strangely quite in line of what I thought the MC would do in this situation, especially after being exposed to the drug from von Doom to "awaken the beast" so to speak.
For people like me who are interested in trying to pull Killian out of his assholish ways and make him a better person, it feels like we really missed an opportunity here to get into just why Mina gave Ian so much rope and what exactly she wants to do abut him going forward.
I did have the same question as well. But then I realize Mira is still trying to identify herself, which is hinted when she admitted she sometimes felt distance with the responses she gave out. I guess she just doesn't truly understand herself in order to make such a decision.
I did have a friend had a similar situation, his SO does raise tons of red flags, and despite of everyone said "just break up with that toxic sludge", he just say "huh.... I don't know...." He gave me a feeling that he wasn't blinded with love or something, he just didn't know what to feel and hence, produce an appropriate response to the situation.
In my head, if Mira is asked what does she like about Killian, I think the first sentence that comes out of her mouth would be "I don't know" then followed by "He is good looking and he is my 1st BF" XD
Just some extra rambling
Speaking of MC's true nature. He was saved by his mother when MC was a kid and become a "decent" adult till the story began. As the subtopic pointed out, motherly love is one of the main focus of this game, I wonder if the future plot requires she to save MC once again and pull him out of this hell hole which is Pale Carnation.
Just my 2 cents
