So much of John's gospel seems to involve conversations that are taking place on two different levels; one is plain and literal while the other is more complex and cryptic. On one level, the conversation between Nathanael and Jesus in John 1:43-51 is a simple one that demonstrates Jesus' unique knowledge and authority which in turn causes Nathanael to confess that Jesus is the Son of God and King of Israel. That alone is a remarkable confession but it seems that the gospel writer may be saying even more than that to us if we listen carefully.
The biggest clue is in v.51 of John 1 where Jesus' words allude to a dream that Jacob has in Genesis 28. In this dream, Jacob sees angels ascending and descending a ladder that is reaching to heaven. God stands above the ladder and reiterates the same promise to Jacob that he had made to Abraham and Isaac before him; that he would give Jacob land and numerous descendants through whom all the peoples of the earth would be blessed. Jacob then awakens from his dreams and declares that surely God was in the place where he had been sleeping.
Once we have been clued in by the obvious allusion to Jacob's dreams in Jesus' words, it becomes easier to notice other parallels between this passage and the story of Jacob, each of them in Jesus' words to Nathanael. In Jesus' first words to Nathanael in v. 47, Jesus declares that Nathanael is an Israelite in whom there is no deceit which is the same word used to desribe Jacob's action in stealing his blessing from his father. Therefore, Nathanael, who confesses Jesus as Son of God and King of Israel, is presented in contrast to Jacob and his descendants, the Israelites (Jacob's name being changed to Israel after wrestling with God just a few chapters later). Even though Nathanael is an Israelite himself, he is set apart by his response to Jesus.
Additionatlly, in John's passage Jesus knows Nathanael before he has even spoken a word and Jesus tells Nathanael that he saw him under the fig tree before Philip had even called him to come meet Jesus. This is in sharp constrast to Jacob's father Isaac who is nearly blind and does not even know one of his sons from the other. Therefore, Jesus and Nathanael are held up as Israelites who are greater than the patriarchs of Israel themselves. There is no deceit in Nathanael as there was in Jacob and Jesus demonstrates just the opposite of the blindness and lack of knowledge that is demonstrated by Isaac.
What is John's point in all of this? John is making a theological point about who Jesus is; he is the patriarch of Israel in a way that Isaac and Jacob never could be. He is the Son of God and King of Israel just as Nathanael confesses him to be. But it is likely that John is also addressing a specific need in his own community. As far as we can tell historically, it seems as if the believers for whom John initially wrote this gospel were in conflict with the Jews of the day who did not believe that Jesus was the messiah. Because Judaism was beginning to define itself as something separate from Christianity, these early Christians had probably been kicked out of the local synagogues where they were accustomed to hearing scripture and praising God. Therefore, John is reassuring these believers that they have made the right choice in following Jesus. Just because they have been excluded from synagogue does not mean that God has abandoned them or that Jesus was a false prophet as they were probably being told by the same people who had expelled them. Instead, John boldly declares that Jesus is the true patriarch of Israel and that Nathanael's response to Jesus is one that these believers should continue to emulate. John is reassuring them that what Jacob only knew in a dream, they have come to know in flesh and blood in the person of Jesus.