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: Peacemaker Kurogane
Foe Yay: Suzu and Tetsunosuke. Come on, Suzu even pretty much comes out and says, after another character asks him why he hates and obsesses over Tetsunosuke so much, that "this isn't hate - this is love."
Oh god, where to start? The whole series is like the living incarnation of Ho Yay. Okita and Hijikata, Suzu and Tetsunosuke, Susumu and Tetsunosuke, Tatsunosuke and Tetsunosuke, Suzu and Yoshida, Heisuke and Shinpachi, etc. Most of the Ho Yay appears to be on purpose, however.
This doesn't actually seem too far off if you consider that homosexual relationships were common during that era, especially with the men from the Shinsengumi. Heck the Japanese even had a term for two male samurai having sex, just look up shudo.
Kogoro Katsura, a politician working against the Shogunate, is depicted in the manga as a small man with large eyes who tends to cry a lot. Ryoma even puts a pair of little dog-ears on him to complete the Moe-factor.
The Scrappy: Hotaru for being a wimpy girl who has a crush on Okita as well as being very clumsy. Tetsu and Tatsu for being attention-hogging protagonists despite being cowardly, impulsive and down right argumentative/ disrespectful to everyone including themselves.
Unfortunate Implications: Every single outwardly gay character is an Ax-CrazyDepraved Homosexual. Most notably Suzu, who was originally a good person when he was straight - however, once he goes crazy, his behavior becomes very flamboyant and he gets gay whenever Tetsunosuke is concerned.
The whole series is pretty much compromised of a bunch of pretty samurai crying and confessing to each other their deepest and innermost feelings of sadness. Oh, and killing people.
Well, except that the terrorists they're fighting kill their friends and family, are trying to destroy their capital, and yet actually believe in the same ideals as them. And that Okita's dying of tuberculosis. And that Kondo, Hijikata, Yamanami, and Okita had to assassinate Serizawa because he used his power for racketeering just a year before the series begins. And the fact that, for them, the penalty for any violation of the Shinsengumi rules or Bushido in general, was ritual suicide. So, no, that they manage to be as cheerful as they are is actually quite impressive.