In general, I agree with @IndigoShirtProd: school settings are just that-- settings. What's more, they are real, contemporary settings: if you want to write a story set in the present day starring people from age 6-18, school is probably gonna be a part of it, whether you particularly want it or not.
Basically, when school stops being a thing billions of children and teens are involved in each year, then we can talk about it being 'overdone'. At this moment in time, it's simply a facet of reality.
HOWEVER, I kinda get where the idea of school settings being 'overdone' comes from...most likely, the plethora of anime/manga where it's basically an aesthetic. ^^; And one that gets leaned on heavily...you can see this in amateur works, where the first few scenes are often just cookie-cutter school manga panels: like, outside the school, the MC waves to her friends while running with her bag in one hand. Or a character sits at their desk, staring out the window, and another character comes up and interrupts their daydream.
Or before you even get to the school, the classic 'character is late and runs out the door with a piece of toast in their mouth'. ^^; It's like, the first thing you see isn't even story; it's just tropes, with the author's characters doing and saying things you've already seen in a hundred other places. I don't know of any other 'genres' that seem to thrive on such repetitiveness...
With that said, I think the best way to approach the school setting (since it's gonna keep being used anyway) is to just...peel yourself away from the tropes. ^^; At the very least, start with a scene that sets your story apart from its thousands of predecessors; do something more unique and memorable than 'character explains their personal motivations while putting on their uniform in the morning'.
All the sameness is cute, but it's not necessary...it's way past time for some fresh ideas.