Is there any reason you think she can't do all that in a harem family, or are you just hating?
It's probably hating...
The thing is it's a story so anything Luxee writes happens.
If we e.g. take the game My New Family we are at the point where the MC from this game is engaged with almost his whole family and the wedding is set for the next update.
I don't see a reason why this couldn't happen in this game too. We also know that Cha has no problem with the MC having more than one GF.
So in the end what I'm expecting is everybody together and happy. Nea included.
I don't think it's the same dynamic as a more traditional family versus a sex game harem. I've played some of My New Family, and it's a fun but silly sex romp. A harem is pretty much the expected outcome, with every character created with that ultimate path in mind. As mentioned before, Nea seems made for something different. Maybe Luxee turns her into a harem girl, but I don't think that would feel like Nea anymore if she just goes along with the harem idea.
Would it be the same thing if suddenly Nea had several boys actively pursuing her, but it was okay because the MC could join her harem and share her with the other men? They could all be one happy family, with the MC and his new "brothers" having their allocated time with Nea. You'd have the romantic love of Nea and the brotherly love of the other men, so it's all cool, right? And for some people, it would be, which is fine. Personally, I wouldn't want that for the MC. I wouldn't want it to for Nea. I suspect the idea of having to share any romantic interest in the game freaks out a lot of players, as it should freak out many love interests in these games, but they think that it's some secret sexual fantasy for women to be part of some man's harem. As stated by many, these games aren't reality, but they often do make attempts at approximating it. When Luxee made the choice to include Nea and focus on trans issues somewhat versus just trans fetishism, it kind of ups the ante on trying to keep the game elements surrounding Nea real.
Nea's on a different level than the other characters in the game, and Luxee has been trying to make a realistic story arc here with a trans woman as the focus. I don't think it needs to be a separate game, but it would help. Unless Luxee can do it just right, it's just not going to feel right, although most people probably won't care as long as they get their harem and can say they've collected all of the girls. But I'd like to see the level of realism continue and a ending for Nea that is good not just for the MC, but for Nea too. I don't think Nea gets her best ending unless its her and her alone that ends up with the MC in her story.
It's weird that I keep arguing for this, because I have no current intention of taking Nea's romance path. But I do like the character enough where I want to see her with the best outcome she can get. And who knows? If it turns out she's not dead and I can interact with her more and get to know her even better, maybe I'll end up falling for her myself. We'll see. I just hope I get the chance for her to not be dead on my friendship path someday.