Are you saying the story sucks when she's not trans or when she is trans?
I dunno, I think the story leading up to that is pretty vague and even the parts where she talks about her parents not accepting her lifestyle could be taken as her gothy, moody, angsty teenage behaviour and not the fact she was trans. Maybe if the scar in her non-trans route was more gruesome it could explain a lot of her shyness, but it's still something I could see someone being very self-conscious about.
I think that the story is substantially less interesting if she isn't a shemale which is annoying because I'm not a fan. As a she-male all the dots connect a lot more, and how repetitive she is makes a lot more sense, as well as her parents disappointment. Because otherwise it's too vague and strains credulity how she puts her down if she was born female, plus the dress scene makes way more sense due to the dick thing.
If she's female, the conclusion to her arc feels significantly less interesting. In both routes, Eve is essentially the same person she began as, but self assured. That arc is more satisfying as a shemale because her journey is perceived rightfully as significantly more complex as such, and thus it feels like a conclusive and satisfying ending, because it also involves the MC showing an unexpected side and 'growing' as a person to be more accepting. If she's not, then it feels like there's no ending per se. You said to a pretty girl she was pretty. You bang her. Feels empty, imo.