And it's not like they just ignore morality, in this game for example the MC gets super pissed at the stalker guy (and for good reason, stalkers are creepy) but fails to see any real issue with any of the fucked up shit he's doing. How exactly he's better than a stalker when he's cheating on his wife with his questionably aged daughters is beyond me, but apparently that's legitimate writing in the authors mind because that's what they went with. If you're going to cast him as a villain then cast him as a villain. There's a game on this site literally called like rape something, I don't remember exactly but you play as some dude and essentially go around raping people. That game to me is far less morally messed up than this one. Why, you might ask? Because it doesn't pretend you're a good person, it doesn't lie to you and have the inner thoughts of the character and the words of other characters somehow imply you're actually a really good guy, it admits you're a sociopathic asshole and therefore the writing is consistent with the experience, as opposed to being a molesting, cheating, raping asshole who somehow the game justifies as a good person.
For the Harem route:
The MC is morally relativistic and doesn't operate according to the Golden Rule, among other things. He's consistently written that way throughout the game, playing one situation and person against another for aiming at his goals.
His sister is consistently written as a manipulator (in a more overt manner, but otherwise similarly goal-oriented and end-justifies-the-means as the MC) who loves her brother and wants sex 24x7 with whomever gets her fancy at the time.
The daughters are written consistently as falling for their father and craving his attention, easily letting him drive their sexual growth and appetites.
Sofi is written consistently as a vulnerable person who falls for the generous MC and the question of how much her sex with him represents love vs her conditioned role to satisfy a person providing for her means is a constant question in the game.
Emily is probably the only character to significantly change: she is manipulated by both the MC and his sister to accept a sharing situation as somehow naturally forming, then to go along with her daughters being included, as well. It could be argued that it turns out Emily had a cuckolding instinct within her and that complemented her growth into accepting the forced situation towards harem-ness, which is an interesting point to consider. Luxee did a subtle job in this area, I feel.
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You seem to be coming from a perspective that isn't defined by the game's Harem path, arguing it should meet your expectations. You're either looking for a different path (such as "The Pure Husband") or a different game.