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.
Base Breaker: Chizuru is an ongoing source of disagreement and debate within the fandom. Many fans feel that she's too weak and passive a Player Character who spends too much of the game playing the role of Damsel in Distress, and that her demon powers provide her character with potential which is criminally underused. Others feel that her serving as emotional support to the Shinsengumi is an equally valid form of strength, pointing out that she's a very proactive woman by the standards of the time period and that a couple of years of sword training would hardly make her equal to the villains, almost all of whom are themselves demons or furies with years of extensive combat training.
Draco in Leather Pants: Kazama has a not-inconsiderable fangirl following, in spite of the looming threat of rape he represents in the common route and the fact that he's the main villain in Hijikata and Saito's routes and the cause of several bad ends in others.
Fridge Brilliance: For all the criticism Chizuru catches for having to be protected so much by the Shinsengumi, the captains' attitudes towards protecting her foreshadow their attitudes toward the shogunate and the Boshin War - in both cases, having committed to the course of action, they refuse to be swayed from it even though they know it puts them at a disadvantage and may get them killed.
In the game's prologue sequence, after Chizuru speaks up for the first time to thank the Shinsengumi for saving her, Saito is surprised, Okita is amused, and Hijikata looks suddenly awkward - reactions which make much more sense once you know that this is the moment all three of them realize she's a girl.
Ho Yay: Inevitable in a Cast Full of Pretty Boys; Okita's idolization of Kondou is a particularly notable example, and there's a lot of it between Saito and Hijikata in the drama CDs and other bonus material, to the point that Okita is able to bribe Saito to turn a blind eye to the fact that he's lost a uniform by giving him Hijikata's book of poetry (with some indications that he's used the medicine made by Hijikata's family as a similar bribe in the past).
Values Dissonance: Chizuru is frequently criticized for not fighting when, as a demon, she has physical potential greater than that of humans. However, the story takes place in Bakumatsu Period Japan, in a culture of very strict gender roles and social classes. In the context of the time period, that Chizuru dresses as a boy and carries a sword, travels to Kyoto alone in search of her father, hangs out with the Shinsengumi and occasionally takes a swing at the villains in a pinch would actually make her quite the tomboy.