Welcome to the Ark has a little bit of a "genius kids" plot device that has the potential to turn porny, but it has a really nuanced treatment of what genius kids should do in the world. At least, compared to other literature targeted at this age group, who are usually just fighting an evil bad guy.

I also have fuzzy but weirdly fond memories of The Chocolate War. Mostly, I remember thinking it was complicated and having to reread it a few years later.