The Mysterious Benedict Society by Trenton Less Stewart-- it's been mentioned here once, but I'm amazed it isn't extremely popular here for rationalism and famous in general as a delightful book.

It's about four orphans who are recruited for a mission against a terrifying organization full of well-dressed people who talk in bafflegab and is led by a vain man who has mind control technology. Not only does the book have appreciation for high intelligence, it has appreciation for different kinds of intelligence.

It's in the romantic tradition (Victor Hugo, not modern romance) of disguises, secret tunnels, and sudden turns of fortune. It has a lot of respect for updating and for checking on whether things make sense.