Before one can attempt to delve into what Nicodemus is supposed to think when he hears Jesus say “This is the way God loved the world…” (John 3:16a), it is necessary to examine other parts of the conversation, as this is a building process. Jesus does not just make this lone statement, but gets there over the course of a relationship and a conversation (of which we have only a glimpse). In the Gospel record, Nicodemus has already spoken to Jesus about the signs that He is doing, with an indication of an assent on his own part that Jesus “has come from God” (3:2b). Again, it cannot be said enough that this was a time of great expectation. Israel is expecting their God to act on their behalf. They are expecting some type of a messiah to make his presence felt.
A widely-held (though certainly not exclusive) understanding about the messiah was that he would somehow be the physical embodiment of Israel’s God. When Nicodemus speaks of Jesus as coming from God, Nicodemus speaks from within this expectation. Nicodemus seems to be making a rather subtle inquiry as to whether or not Jesus was (or at least thought He was) the messiah. His own words about the Creator God of Israel being with Jesus would seem to indicate that he believes that this is a strong possibility.
How does Jesus respond to what Nicodemus says? He responds by making reference to the Jewish, messianic hope that the God of Abraham, Isaac, and Jacob was certainly going to fulfill His promise and establish His kingdom. Keeping things simple, this would entail firstly the removal of Roman oppression, and secondly the subjugation of Rome to Israel, as Israel was to be elevated above all nations, with its messiah installed and recognized as king. Jesus, presumably, is fully aware of the Jewish hope and would have shared in that hope. Indeed, by His own words that are to come, one can see that He believes that He is fulfilling the Jewish hope of kingdom.
In demonstration of this awareness of the kingdom hopes harbored by Himself and by His people, Jesus says to Nicodemus: “I tell you the solemn truth, unless a person is born from above, he cannot see the kingdom of God” (3:3). After a response from Nicodemus which serves to reveal just how truly puzzling this statement was, with its inclusion of being “born from above,” Jesus continues and says, “I tell you the solemn truth, unless a person is born of water and spirit, he cannot enter the kingdom of God” (3:5).
Clearly, Nicodemus is confused by Jesus’ speech here, and one would have to imagine that he would not be alone in his confusion. Even Jesus’ own disciples, though they are with Him all the time and had the chance to hear Him speak (and likely expound on His thoughts) on a regular basis, as He likely made similar intriguing and potentially confusing statements on that same regular basis, were routinely perplexed by what He had to say and found themselves in need of private explanations.
Granted, as a Pharisee and an esteemed member of the Jewish ruling council, Nicodemus was no doubt part of the elite and educated citizens of Israel. It is unlikely that he was an intellectual and theological slouch. However, the Gospels report that Jesus routinely stumped even the most elite with His statements and His questions. As he hears the words of Jesus, one can surely envision the confused expression that rested upon Nicodemus’ face, prompting Jesus to say “Do not be amazed” (3:7a) at these things that I have said to you.