For example, I think stoic MLs are supposed to be like they only show the MC or close ones their soft side, but more often than not, in an effort to maximise that "you're the special one" they end being up being completely rude or psychotic.
Like if a character is kind, some writers made the FL nice but they write novels with the FL getting r*ped
TRUE. FL is so kind that she won't fight back against her rapist because she doesn't want bad things to happen to the people around her type beat. I believe the "Loner MC" shit is misused. THE MC IS NOT A LONER IF THE MF HAS 4 FRIENDS AND 3 OF EM ARE WOMEN AND THE 1 GUY HAPPENS TO BE THE MOST POPULAR GUY IN CLASS!
Harem. Whether it's Jpn isekai, Cn/Kor martial arts, or just everyday theme. It's all been explored and still going strong in novel and manga.
Tsundere!! Just because she's rude doesn't mean she's tsundere!! For example, she laughed at the MC for having social anxiety after bullied him for so long then she was like "Tehee~ I like your expression~ ufufu~", and the MC suddenly went "OMG she bullied me because she likes me?!"
Having been in that position in high school, I really just wanted to be left alone but when the popular kids want to hang out with you, refusing would only get you bullied so why go through that? Same with work, if you can't get along with people at the bare minimum you probably won't last long. An ounce of prevention is worth a pound of cure. It's especially helpful to be next to an extrovert who will put in most of the effort and you just have to tsukkomi them occasionally when they say something really dumb. It's annoying but school and society target people who are alone...
The unreliable narrator is one I feel is definitely underutilized. I am a big fan of Kumo Desu and the zany crap the FL gets in to. I would love to have more unreliable narrators, and it feels like stories that do use an unreliable narrator aren't marked as such half the time.