I love John Chapter 3, over the years I have collected insights to it. Here Jesus is specifically pointing out to Nicodemus that one needs to be transformed by the Holy Spirit, and we cannot be presumptuous that we know how God works or even the Holy Spirit. We need to cultivate a relationship with the Holy Spirit by waiting on him and with Jesus by reading how Word. With both these we need to re-evaluate each thought and its source. Is it of the world? Does it belong to our own spirit, or is the source God.
We have travelled many a miles from what Jesus said, and what he meant, and we have lost the sense of what he did say and within the context he has said it. We have become influenced by the communities that we lie in and their general everyday wisdom, and have taken it and ascribed it to Jesus. This was the same story when Jesus told the Pharisees that Divorce is not what God instructed them at Sinai, but it was Moses who let them have it, because they preferred to remain ignorant of a relationship with God.
This is the message Jesus gives the soul seeking Nicodemus. Be born anew, but to be born you need to be naked/bereft of everything. So also he tells Nicodemus, cast away your intelligence and understanding. Stop being presumptuous and wait on God and receive his wisdom. Bible Reading and Study without Jesus besides you to help understand context and focus of his words, we will miss the mark. It is a tough challenge to let go and wait on God to guide, but not impossible. Approach him with this as your desire, and ask him to help you. He will bless your desire.