Adaptation Displacement: Even though the visual novel and OVA received releases in the United States, Requiem for the Phantom is the most popular version of the story. This is a result of the fact that the visual novel is very rare to find a copy of and the OVA only adapted the first act of the story. The OVA at this point seems to have been widely forgotten.
In Requiem for the Phantom the third act of the story was very divided among viewers. Either you like it for being a climatic way of wrapping up the story with many intense and tearjerking battles, or dislike it for shifting the setting to that of a Japanese high school and the last few episodes killing off a majority of the main characters.
The ending to Requiem for the Phantom has had divided interpretations. For some Zwei's ambiguous death was effective as he had nothing else to live for and as an assassin his past would eventually catch up to him. However for others the fact that it occurred right as the anime adaptation was about to end and he had already been through enough suffering made it feel forced.
Complete Monster: In the first 10 minutes it is established that Scythe Master used a combination of drugs and hypnosis to erase the main character's memories just because he wanted to test a new theory. He then leaves the main character to train for months in the Mojave desert with no contact from the outside world. This was the second experiment. The first person he experimented on he rapes, brainwashes, trains as a serial killer and treats like property, oh and the girl was twelve when he started this. A third person he experiments on he doesn't drug or rape, but he does basically lie to her about events, encourages her growing hatred and turns her full Yandere just to mess with the main character. Oh and while he is doing this with her, he is repeating his first experiment, six times over, just in case.
Darkness-Induced Audience Apathy: Being written by Gen Urobuchi this one is a given. Being one of his earliest works it is one of the darkest narratives he has ever worked on. There's hardly any comic relief, and there is always a sense of omnipresent danger. Taken Up to Eleven in Requiem for the Phantom which adapted the most depressing route of the visual novel which involves a majority of the cast being killed off.
Replacement Scrappy: The first opening theme Karma is a foreboding song that does a great job at building atmosphere for the series and unlike other anime opening themes it plays for 19 episodes instead of 12-13 like most two-cour series. Needless to say replacing it with a more upbeat ALI Project song in the second half did not go well with fans.
The Scrappy: Mio Fujieda especially because she plays an important role in the very divisive third act of the story. While Ein and Cal had interesting backstories and relationships with Zwei, Mio is just a normal schoolgirl that suddenly appears in the plot. The fact that her most important role in the story is getting kidnapped by Cal and having to be rescued by Zwei didn't really help her either. However some were relieved to see that she was one of the few characters to survive the plot and have a happy ending in Requiem for the Phantom.