I like the meat of the writing of the MC a lot when you take basically any scene he's in individually. It's the portrayal of his morals and ethics overall that strike me as a bit off. I feel like the main game's protagonist is a hyper-idealized individual, who's far too competent and not particularly human. In truth, if anyone was going to secretly turn out to be a god, my money might've been on the MC if not for the clear characterization telling us otherwise, and the contract.
Even in the Ruthless route this gets turned on its head in the worst way rather than the MC actually being base in some way. His reasons for going off the deep end are specifically because of delusions of moral superiority. Even as a monster, he is evidently not capable of doing what he thinks is the wrong thing. That feels particularly alien to me.
There's a lot of talk about him putting aside negative thoughts or impulses for the sake of Asterion in the main route, but what I find odd is that he simply doesn't have those thoughts expressed at any point. And like someone said prior, when he's put into difficult situations he responds with not just the patience of a saint, but the competence of a trained psychologist, in most if not all circumstances, such that he never actually feels like he has to deal with Asterion's clear trauma in the way that someone normal probably would. There's no accidentally triggering him, or just even being around him when he's triggered. He shows sadness, but not anywhere near the shaky, aversive, shut-down he does in the ruthless route for instance, and sidestepping that sort of thing completely isn't something someone easily does.