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, because she's a regular Damsel in Distress with timid, unconfident dialogue despite being the Player Character. On one hand, Chizuru is a proactive woman by Imperial Japanese standards who goes out of her way to search for her missing dad and support her love interests. Male characters outright tell Chizuru to stay out of fighting and important events because she is a girl, and they don't seem to mind that they have to protect her. On the other hand, Chizuru is a demon with superhealing and at least one instance of superspeed. Suffice it to say that her powers are incredibly underutilized.
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: Poor Chizuru is called weak, stupid, slut and Faux Action Girl for not fighting... and the people who bash her "conveniently" forget that, well, this story is set in what would soon become Imperial Japan. If gender roles have evolved slower in Japan than in other parts of the world, imagine how more rigid they were back then. Please make some contextualization before judging a girl who lives in an historical moment with completely different values from those we have now.
Lampshaded and deconstructed in Chapter 4 of Sanosuke's route, when Shiranui starts shooting at Chizuru. She surprises herself by instinctively using superspeed to dodge a bullet, without realizing she had that power. Shiranui points out that as a demon, Chizuru doesn't have to abide by human cultural standards and could become a powerful fighter if she tried to train her demon superpowers. She never does.