Setting wise, because high school is culturally equivalent to American college for the average "wage slave"/office worker. It's simultaneously your first and last breath of freedom untill retirement, but even moreso than life after college in America given Japan's piss poor working conditions. Its the same reason, really, we get a lot of movies and TV shows involving college.
The inappropriate situations... well we'd have to really get into Japan's view and infantilization of women to truly get insight. So I'll just say that the unfortunate situations being a standard can be attributed to appealing specifically to otaku who have interest in upskirts and molestation of anime girls, and a general sense in Japan of "what you do behind closed doors is your business as long as you contribute your dues to society and don't rock the boat". So it just sells and with little pushback.
Combine the two for maximum profits, you get uncomfortable situations... with high schoolers.
