MM!/YMMV

Complete Monster: Yoshioka, girlfriend-beating kickboxing loser with an undeservingly pretty face.
Jerkass Woobie: Mio; she gives off such sad image on several occasions throughout the series.
Leave the Plot Threads Hanging: In the anime, only Mio's story is really "resolved" by the end. Unfortunately, we may never get any conclusions at all due to the death of the author.
Les Yay: Yumi's "massages", Michiru's voyeuristic photography, and the "Heaven Side" opening featuring Mio and Arashiko in... interesting poses with each other.
Motive Decay: Mio started tormenting Tarou on the principle that there is a level of pain that even he could not stand. After a certain point, she just seems to be doing it because she likes to.
Unfortunate Implications: An attempt at using hypnotism to "fix" Taro's masochism leaves him with various oddball fetishes as his perversion finds other ways to slip through his subconscious. This is fine, until the last version -- in which he's perfectly, absolutely normal. Except he's gay, and madly in love with his best friend. This is considered vastly worse than his crippling masochism fetish, although to be fair, the people who think this are part of the Love Triangle.
Values Dissonance: Taro's reaction to Yuno being stalked by her sempai is not to call the police or tell an authority figure, but rather to beat up the guy himself. This is very much so a Japanese ideal of keeping sexual assault-related problems out of the public eye, as to discuss them is seen as shameful on the part of the woman. Furthermore, Taro upholds classically prized Japanese masculine behavior by defending Yuno's honor independently without relying on external help.