Hmmm ... yes and no? More of an anime thing imo, but I do feel like there's a contrived tendency for everything to take place in a high school, even if it has no inherent reason to (and sometimes a lot of reasons to not). You have cooking high school, sports high school, music high school, military high school, adventurers' high school, villains' high school ... like, can we at least get some universities instead?
Bonus points for being set in, say, a medieval fantasy world where education for teens have literally no reason to resemble a modern Japanese high school 
I don't think real-world school stories is overdone though; if anything, it's an age distribution issue, rather than a location distribution issue - that's just what happens when most comics and anime (including those set in the modern real world) are about young protagonists ¯\_(ツ)_/¯