So, that's some examples of schools that aren't terrible
I don't know a lot of them really can lean either way.
Haruhi's school is good on paper but honestly the teachers are probably the biggest "I just don't care" I have ever seen... With even strange people being able to walk in and out of the school entirely unhindered... as well as rather open instances of outright assault, sexual abuse, and I think even kidnapping and they are like "ehhh, we will let it slide".
Nobody hears about the school from deathnote
Because it is rather superfluous to the manga except that it hosts a handful of scenes that really could have happened anywhere.
It is why I added the "with focus" aspect into it. Since most anime and mangas feature a school or university in someway, but rarely really highlight it other then using it for a scene or two.
Honestly you probably never even see the cafeteria of the school (though I think Japanese Highschools might not commonly have a cafeteria)
How about the school from Alien 9?
It really isn't fair to say a school sucks just because it is in a series where terrible stuff keeps happening.
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Also I am going to double whammy and put Zach Bell and Persona 4 anime into the same "terrible school" category.
But in their cases it is because the schools keep hiring the worst faculty ever devised... almost consistently.
And oddly enough... They both hired a woman who seems to like flirting with her underage students. Heck I wouldn't be surprised if she was the same woman.