I am also Czech and do NOT have similar experience. I am very satisfied with the level of education I received and with the environment I was able to be part of at my university in Prague.
Are you sure? If you've attended any of the top 3 universities, you just were shielded from it; generally IT/math/science related faculties work well, it's the social-related faculties where it works really badly, but still, you won't see it as a student. I'm happy to tell you more in private.