The real problem for me, is that while Stewart's story is technically good, it lacks soul, or more specifically, it lacks an understanding of a child's soul. This is an intangible quality that I don't think an author can learn. Take, for example, A Wrinkle in Time, a warhorse in children's literature. Madeleine L'Engle tells a very sophisticated story from the perspective of a cranky, misfit girl named Meg. Meg is the older sister of an extraordinary boy named Charles Wallace (who has more perspective at six than most people have at sixty). L'Engle's Meg never sounds like an adult's idea of a cranky, misfit girl, just as Charles Wallace never sounds like an adult's idea of a six year old savant. They sound like real people, not adult constructions. All of Stewart's extraordinary kids - from Reynie Muldoon, the moral compass and natural leader, to George "Sticky" Washington, the genius beset by nervous ticks - feel like an adult's "Very Clever" conception of very clever kids. There's a fug of grown-upness over the whole thing and it just doesn't work.
The other problem with the story, is that there's a huge bloody build-up to what should be a huge bloody show-down, but the final resolution happens off-screen, AND it's not even the kids who achieve it. An adult, the eponymous Mr. Benedict, mysteriously dismantles the Evil Machine of Doom (tm). This results in an Ok-so-I've-read-and-read-and-read-and-THAT's-the-resolution?!? feeling in the reader. Then we scoot through the denouement, and because of some serious authorial strong-arming, everyone ends up happy. Deux ex Machina is splashed all over this thing. It's as if Stewart got his characters right into the thick of the action, and didn't know what to do next - there's too much machination, and too little imagination to make the thing take off.
All in all, The Mysterious Benedict Society is a great idea, and there is a lot in it that works - obviously, people like it as it's selling like a Bestseller. Still, it missed the boat for me. There are a lot of children's books out there that work (anything by Roald Dahl, Coraline, and The Phantom Tollbooth to name a few), and they work because they are genuine things - stories that appeal to the instinctual fears and fascinations of children. It's not enough to be clever, you have to be genuine, and that's where The Mysterious Benedict Society, which is ever-so-clever failed.