I can't speak for anyone but myself in particular, but for myself and at least some people I've witnessed(didn't keep track of usernames), the bold parts a severe issue with this story, and why a friend route may actually make more sense. You have the story focused around one character that not only is written in a rather logical and somewhat realistic sense, but is EXTREMELY vulnerable emotionally, to the point of self-destruction upon rejection, inside a game that actively blocks progress if you don't commit to building a harem. It feels like with Nea, the intent is to draw you in and make the interactions with MC believable. The issue is, a character like this would crack in the exact same way - possibly worse - if led to believe their love interest was building a harem with his family, their bullies - anyone he can stick his dick in, really - the entire time that they felt they had found "the one" and that they were someone else's "one." One can only suspend their disbelief so far, and I'm pretty sure a good deal of people would not be able to suspend their disbelief that, upon finding out MC is balls-deep in so many people, Nea would just say "fuck it" and roll with it.
I don't follow this thread endlessly, just pop in every now and again, but over the months, I've seen this brought up a few times, and it's never actively addressed; all I see is people get labeled as "transphobic" and the legitimate criticism is subverted. Even people who have said they really like the Nea character, and would love a Nea-only game, but that she doesn't fit into Apartment 69 are shut down in identical fashion. (Which is rather confusing, seeing as it seems to me that Luxee has written Nea as the main love interest and has given her the spotlight far more than anyone else; if this is the case, I would think Luxee very well might enjoy making a Nea-only game.) Hell, I'll probably be called transphobic for this post for suggesting a Nea friend route could have made sense, but the game is now at a point where neither a friend route nor love route will make sense, should the harem aspect be kept in place.