The main reason for Joowon and Haesoo’s relationship being messy is because they decided to keep it undefined due to the incest taboo. Like the whole point of this story was showing how they didnt want to face the consequences of their relationship (consequences such as haesoo losing his mom), due to the TABOO, and thus they entered this unhealthy state of ambiguity— where the only way to actually express their love was through manipulation, jealousy, possessiveness, etc. the lack of communication and hurt all stems from the ambiguity too. So as far as we see, their relationship wouldve been fairly decent (not “perfect” obvs, cause theyre still humans and have flaws) if not for the taboo.
This goes to show that the ending you get is not always the ending you want. Yes, it's frustrating but neither of the relationships were healthy to begin with. Even if you take the incest out of Haesoo and Jowoon’s relationship, it still wouldn’t have been a pretty one. And then there’s Haesoo’s relationship with Taku that was bound to end up in flames eventually no matter what.