Just saw this and Little Man Tate pretty much back to back
And this movie is 10 times better. No, the movies aren't the same, but they have similar themes - kid genuises and the battle for their souls. There are a few reasons this one is much better.
First and foremost are the kid actors themselves. This kid is cute; the other one is unusual-looking. This kid is sweet, and, as Joan Allen succinctly put it, "decent." You like him; he's a good kid, one you'd like to have your kid have a playdate with. The other kid is weird, strange, probably autistic, and has no social skills whatsoever.
But it's also the story. The battle over the kid's soul is played out more effectively here than in Little Man Tate. You care more about it here because you care more about the kid here. You also care more about it here because I think you can identify with the parents more. Here, they're middle-class parents, trying to afford their kid whatever advantages they can. There, Jodi Foster's character is a perpetually out-of-work single mom, too proud to have her kid be away from her, even if it's for the kid's own "good". I don't think we identify with that much.
I want the doctor to take your picture so I can look at you from inside as well.