A big part of what makes school uncomfortable is related to the physical space in which it takes place. As you said it, it has many attributes of a prison. Too crowded, which means too noisy. Closed, which means there's no room for breathing when things get socially too heated. Little privacy. In many places of the world, included rich ones, schools are in a state of disrepair. And in general, they display a situation where users have no input in the design process.