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.
Crowning Music of Awesome: The anime plays the music too quietly to appreciate it, but the soundtrack CD really shows how good the music is. Even in the anime, you can still hear the awesome if you pay attention. Try listening to the music when Takatori Reiji speaks. Also, Piece of Heaven
Die for Our Ship: Nearly any female character who has any kind of romantic connection with any of the leads comes in for hate from the fandom (in spite of the generalfutility of shipping in Weiss). Tot, Ouka, and Sally are probably the worst cases.
Harsher in Hindsight: The scene in the Kapitel finale where Weiss (and Aya most bluntly) tell Birman not to come on the mission with them because of her injuries gains a much harsher sting in light of Dramatic Precious, in which she shoots herself with Aya's gun after being tortured by Ayame, because Weiss insist on rescuing her and her injuries are slowing them down.
Replacement Scrappy: Sena has been accused of being Omi's, based on his taking over the team's "kid" role and bearing a resemblance to Omi's Gluhen design. Chloe in Side B is more of a Suspiciously Similar Substitute: he shares many qualities with Youji, but Side B fans love him for it.
They Wasted a Perfectly Good Character: Botan, we hardly knew ye. But any man who shows up unexpectedly in his subordinates' cars and eschews motivational speeches in favor of beating Aya up until he agrees with him is good in my book.