Jesus surely sees something special in this candid chap from Cana: “Here is truly an Israelite in whom there is no deceit." Jesus gives him credit for stepping forward in faith, even though Nathanael has doubt and skepticism. Jesus pays him this compliment because Nathanael is at least open; he’s at the very least going to check it out — see what Jesus is all about.
Jesus loves it, and loves him. This willingness to step forward in faith is a commendable quality, one that is every bit as impressive as a top SAT score. But Nathanael was probably not a brainiac — but who knows? He did have faith. He may or may not be in top intellectually, but clearly he’s in the top of the faith life.
He’s perceptive: “Rabbi, you are the Son of God!” says Nathanael, after Jesus divines his identity, having spotted him under a fig tree. “You are the King of Israel!”
And Jesus answers, “Do you believe because I told you that I saw you under the fig tree? You will see greater things than these." Jesus invites Nathanael to continue to follow him in faith, and he promises that he will see even more amazing things, including the opening of heaven, and the ascending and descending of the angels of God.
It is clear to Jesus that Nathanael is only at the beginning of his faith journey. But if he continues to step forward, he will see things that will make him even more faithful.