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.
YMMV: I Have No Mouth And I Must Scream
Angst? What Angst?: The boy in Benny's scenario, who never mentions his mother again after learning of her tragic death.
Anti-Climax Boss: The Yellow Rapist in Ellen's scenario. All you have to do is select a dialogue option where Ellen stands up to him, and he falls apart after one strike.
That may have been the point. For all its power, AM does not have the ability to resurrect the dead. It can only create illusions of people, and some of these illusions would just fall apart if attacked. AM thought it could just scare Ellen into submission with an illusion of her rapist, but it did not take into account that she could fight back against her rapist.
Complete Monster: AM, without question. Ultimately his downfall, as two of the Logic Bombs used to finally defeat him revolve around compassion and forgiveness, things he's incapable of understanding.
Also a few human characters who are encountered in the game as Virtual Ghosts. There's the nazi scientist Dr. Mengele, Gorrister's mother-in-law Edna, and the "Yellow Rapist", who not only violated Ellen sexually but physically tortured her and did the same to twenty other women.
Esoteric Happy Ending: Ted actually manages to triumph over AM and prove the computer is not the all-powerful god it set itself up as by killing all the other prisoners and freeing them from their torment. A combination of the fact that the price of this is being turned into a helpless jelly-thing to prevent him from ever winning again, and the fact that he's an Unreliable Narrator who's become too cowed by AM to realize he won tends to hide the "happy" part from most readers.
Oh, and there's the fact that for all the Moral Event Horizon AM crossed, it manages to get off with little more than a bruised ego.
Unfortunate Implications: The one character most changed for the game is Benny, who went from an (formerly) openly homosexual scientist to a straight military officer. This is more than a bit odd, considering all the other controversial issues which were included. Rape and Holocaust? No problem! Homosexuality? We can't have that! To be fair, one of the game's lead designers later expressed regret for passing up on the chance to explore homosexuality in a video game.
The Woobie: Who cares about anything bad that they've done. C'mon, how could you not feel sorry for them?