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.
Memetic Mutation: That one scene from the OP, where Mariya rips open Matsurika's top. It has been re-done/photoshopped with countless other fandoms. Ditto the shot of Mariya playing Matsurika like a guitar.
The Scrappy: Both Kanako AND Mariya have some hatedom from both sides (the former for being a bit of pervert, and a later being a sadistic misogynist crossdresser who manages to fool everyone in an all-girls Catholic high school).
Unfortunate Implications: Mariya not only physically and emotionally abuses Kanako for having found out his secret, but he also threatens to rape and/or burn her to death several times. And we're supposed to find either his actual abuse or his threats of abuse/rape/death funny? Specially after poor Kanako runs away crying to the Virgin Mary and wondering what on earth did she do to deserve it? Kanako is quite the pervert and a Butt Monkey, but no one deserves such shit.
The deal about the Shidou twins having to crossdress for three years as a part of an inheritance competition can easily be seen as their grandmother (the person who set said inheritance competition in her last will) being transphobic and forcing her views on gender roles and stereotypes on Shizu and Mariya. Not even the fact that Mariya accepted the deal on the grounds of him loving said grandmother can excuse it.
The Woobie: Kanako. Especially when the abuse and misfortune she suffers goes too far.