From the Wall Street Journal's Speakeasy:
Question: What’s the secret to casting good kid actors?
JJ Abrams: April Webster cast the movie with Alyssa Weisberg. They saw thousands of kids. There was something about Joel [Courtney] when he came in, there was just a sweetness to him. Sometimes when you use professional actors there’s a posed sweetness. And Elle Fanning is unbelievable.