The characters in those fics are also vastly more intelligent and conscientious than average. True, current school environments are stifling for gifted kids, but then they are also a very small minority. Self-directed learning is counterproductive for not-so-bright, and attempts to reform schools to encourage "creativity" and away from the nasty test-based system tend to just be smoke-screens for any number of political and ideological goals. Like the drunk man and the lamppost, statistics and science are used for support rather than illumination, and the kids are the ones who suffer.

There are massive structural problems wracking the educational system but I wouldn't take the provincial perspectives of HPMoR or related fiction as good advice for the changes with the biggest marginal benefit.