The main thing for some people I think is that it was all supposed to be avoidable content, which is kind of standard for that kind of thing and what was promised by Luxee. Making the character the central love interest and having so many paths go through Nea complicates things, and I seem to recall that you broke early versions of the game if you avoided Nea altogether. I could very well be remembering that wrong though. It was impossible to progress unless Nea was involved. If you look at Luxee's website, the mom is actually the promoted character in some places, which maybe led some people to expect a different focus as well had they not known the history for the game. We all knew Nea would be in it, but I don't think it's something that actually gets advertised that much other than Nea's picture on some banners.
The "friendship" route with Nea also involves catching her masturbating with the MC's underwear, which may have been more than people expected to see when they thought the trans content was optional. It's like a game with optional incest content yet you walk in on your sister masturbating in your bed moaning your name before opting into that action. It wasn't a huge deal for me, but at the same time the entire scene was awkward in itself. I guess I never really saw girls as being obsessed with men's dirty underwear. Being a wearer of said underwear, I'd stay away from even my own once I take it off. Not being female myself but trying to extrapolate female behavior from what little I know about them, it would have made more sense to me for Nea to stumble across a photo of the MC in swim trunks or something while he was out, or just crawl into his bed or put on a shirt he had worn earlier before masturbating. And then the scene kind of leads into more awkwardness and Nea's suicide if you choose just to be friends.
I also wish the questions had been clearer. I kind of stared at them when they came up, and they just seemed worded... weird. Unclearly. Certainly it didn't imply there's be bad stuff if you picked the friendship route at the end. It just said Nea wouldn't be in love with you anymore. All we really needed were "I love Nea" and "I want to stay just friends" as options, and the friends one not lead to suicide unless that's just unavoidable on any route or the MC messed up in a big way. Although the way the questions were worded, I'm still not sure if we were opting into sex with one of the choices or if there was going to be a third "friendship" question further down the road.