These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Bellisario's Maxim: How else are we expected to believe that parents are not getting their kids out of this school ASAP?
For that matter, why doesn't anyone call the police?
The owner of the Mega Corp. financing the school is said to be perfectly willing and able to destroy the lives of anyone who won't go along with his plans.
Shocking Swerve: Chapter 22. Tsuki is the Big Bad.What? It doesn't help that the whole thing is presented as a dream of Sora's. Because she fainted from learning that.
Unfortunate Implications: Almost every single guy is a sadistic, misogynistic asshole. Whether or not "He's only doing it because of peer pressure," "He's afraid to go against the system," or "Those who try are doomed to fail, so no-one tries" mitigates this, or is just another kind of Unfortunate Implication, is a YMMV on its own. Averted later.
The final chapter. Apparently easily forgiving someone who beat you and tried to rape you is a good thing. What.
What Measure Is a Non-Badass?: Tomoko is a fourteen year old girl in a nightmarish situation... A number of forum goers have decided that she is a useless coward who shouldn't have the privilege of being Sora's slave and deserves whatever happens to her next. Some of those same forum goers have complained about the male characters all being utter bastards. And then there are the reallyscary internet dwellers (thankfully not many) who actually think a school like this is a good idea.
The Woobie: Reversed. Yuki starts in a state of utter misery where her only comfort is a picture of Sora and Koharu. She becomes one of Sora's most confident allies and goes on to take a beating to protect another student.
All the girls, really.
Special mention goes to Tsuki. Orphaned as a child, taken care of by an abusive relative who is essentially the founder of the oppressive Iwahijiri system. She goes insane when she sees Sora "betraying" her, out of fear of being left alone again. Then, she's left with the choice of perfecting the Game, or allowing Sora's life to be ruined from the stigma of the incident. She chooses the former, but tries to tilt things in Sora's favor as much as possible (by appearing as X, and by bugging the system so she has the glove), but people still bash her and call her a heartless bitch because she helped complete the system, ignoring that she had little choice, and that she's been actively interfering with it the whole time.