No offense to you, because I know this doctrine you're defending is not your invention, but this teaching amounts to a incredibly profound 'duh' moment. "Gee, we have to be born to enter the kingdom of God? Thanks for warning us Jesus."
Again, do not take offense, that is not aimed at you, but rather at the silly doctrine this is that circulates in our churches.
The main problem with the water being a metaphor for literal, natural birth (or metonymy, which ever it is in the case of literal birth) is it does not take into account the proselyte who joins himself to the nation and kingdom of Israel. But if the water is understood to represent joining the nation and kingdom of Israel through an outward repentance to the righteousness of God through water baptism then it does account for the foreigner who joins himself to the nation and kingdom of God's people.
Take the 'literal' aspect out of the birth Jesus is talking about and I think you are getting close to what Jesus was trying to tell Nicodemus. Remember, the problem Nicodemus had was he was also thinking in terms of the literal and not the spiritual.