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I wrote on this question of anothen a couple of times a while back. Here is a slightly refurbished rehash of those comments:

Louw-Nida treats the expression "gennao anothen" ("born again") as a composite with idiomatic value, which may offer us a better way to understand how "anothen" could take on a specialized meaning when linked with "gennao" ("born").

41.53 γεννάω ἄνωθεν (an idiom, literally ‘to be born again’); παλιγγενεσίαa, ας f: to experience a complete change in one’s way of life to what it should be, with the implication of return to a former state or relation—‘to be born again, to experience new birth, rebirth.’
γεννάω ἄνωθεν: ἐὰν μή τις γεννηθῇ ἄνωθεν ‘unless a person is born again’ Jn 3:3. It is also possible to understand ἄνωθεν in Jn 3:3 as meaning ‘from above’ or ‘from God’ (see 84.13), a literary parallel to the phrase ἐκ θεοῦ ἐγεννήθησαν in Jn 1:13. In Jn 3:3, however, Nicodemus understood ἄνωθεν as meaning ‘again’ (see 67.55) and γεννάω as ‘physical birth’ (see 23.52).
παλιγγενεσίαa: διὰ λουτροῦ παλιγγενεσίας καὶ ἀνακαινώσεως ‘new birth and new life by washing’ Tt 3:5. The metaphor of ‘new birth’ is so important in the NT that it should be retained if at all possible. In some languages ‘new birth’ can be expressed as ‘to cause to be born all over again’ or ‘to have a new life as though one were born a second time.’ See also 13.55.

So you see, sometimes this selection of alternate meanings can happen as a direct function of idiom, i.e., a secondary sense is promoted to a primary sense by appearing in partnership with another word.

For example, a chip is an electronic circuit or a bit of chocolate or otherwise a small bit of some physical thing, unless it's on your shoulder, in which case it's a grudge. Imagine trying to translate that from English back into Greek. No native Greek reader would get it, because the idiom changes the meaning of "chip" so dramatically.

However, it is true "anothen" by itself can refer to some kind of "above-ness." But which one? Place, or Time. From the Intermediate Greek-English Lexicon (IGEL):

ἄνωθεν, -θε, (ἄνω) Adv. of Place, from above, from on high, Hdt., Trag., etc.; ὕδατος ἄνωθεν γενομένου, i.e. rain, Thuc.: from the upper country, from inland, Id.
2. = ἄνω, above, on high, Trag.; οἱ ἄν. the living, opp. to οἱ κάτω, Aesch.:—c. gen., Hdt.

II. of Time, from the beginning, Plat., Dem.:—by descent, Theocr.; τὰ ἄν. first principles, Plat.
2. over again, anew, N.T.

This is something one has to respect when dealing with the Greek. They have a very flexible way of reusing parts of speech in both temporal and spatial settings, and within those categories there can be a wide range between the concrete and the abstract. In this case, as the IGEL entry demonstrates, "anothen" can be either spatial above-ness (simple "above"), or temporal above-ness, i.e., going back to Time Zero and starting over, from which we get the simplified "again."

In John 3, the conversational dynamic cannot be ignored in sorting this out. Whatever Jesus meant by anothen (or its Hebrew or Aramaic spoken equivalent), Nicodemas didn't pick up on the spatial meaning "above" at all. He is clearly thinking of a temporal reset, but it is degenerate from what is meant by "born again," because, as an idiom, and especially among evangelicals, it implies both the temporal and spatial aspects, i.e., being born again is both from above and a second birth event. Therefore it seems likely it was something of a double meaning, where Nicodemas got derailed by taking it in a strictly temporal, and strictly materialistic, sense. Jesus then had to rebuke Him for his lack of insight into the Old Testament teaching on the spiritual aspects of the new birth, which Jesus unfolds as birth by water and by "pneuma" (spirit or wind), and as the following passages testify, Nicodemas, as a teacher of Israel, should have associated those metaphors with their prophetic counterparts, of which the following are only a small sample:

Thus saith the LORD that made thee, and formed thee from the womb, which will help thee; Fear not, O Jacob, my servant; and thou, Jesurun, whom I have chosen. For I will pour water upon him that is thirsty, and floods upon the dry ground: I will pour my spirit upon thy seed, and my blessing upon thine offspring: And they shall spring up as among the grass, as willows by the water courses.
(Isaiah 44:2-4)

... which makes clear that water can represent God's Spirit, applied to thirst, not clean skin, or it can be God's blessing, the source of nutrients that make living things grow, etc.

Then said he unto me, Prophesy unto the wind, prophesy, son of man, and say to the wind, Thus saith the Lord GOD; Come from the four winds, O breath, and breathe upon these slain, that they may live. So I prophesied as he commanded me, and the breath came into them, and they lived, and stood up upon their feet, an exceeding great army.
(Ezekiel 37:9-10)

... which makes clear that "pneuma" can be representative of God, by His breath, bringing new life into the world, as the new birth does.

Still, whether Jesus was holding Nicodemas accountable to know about these specific passages or other similar passages I cannot say. There are other possibilities. For example:

Therefore say unto the house of Israel, Thus saith the Lord GOD; I do not this for your sakes, O house of Israel, but for mine holy name's sake, which ye have profaned among the heathen, whither ye went. And I will sanctify my great name, which was profaned among the heathen, which ye have profaned in the midst of them; and the heathen shall know that I am the LORD, saith the Lord GOD, when I shall be sanctified in you before their eyes. For I will take you from among the heathen, and gather you out of all countries, and will bring you into your own land. Then will I sprinkle clean water upon you, and ye shall be clean: from all your filthiness, and from all your idols, will I cleanse you. A new heart also will I give you, and a new spirit will I put within you: and I will take away the stony heart out of your flesh, and I will give you an heart of flesh. And I will put my spirit within you, and cause you to walk in my statutes, and ye shall keep my judgments, and do them. And ye shall dwell in the land that I gave to your fathers; and ye shall be my people, and I will be your God.
(Ezekiel 36:22-28)

(hat tip to redleghunter for finding this)

... which is a wonderful passage because it directly associates water as a metaphor for cleansing from sin with the change of heart and the giving of God's spirit, which is precisely what evangelicals mean when they refer to the new birth.

But clearly, whatever it was Nicodemas missed, it was something Jesus considered obvious teaching of the OT, something no true teacher of Israel should have missed, concerning the new birth. And no OT teacher taught or should have taught that physical water baptism was necessary either for salvation or even for true cleanness before God. Remember how the Pharisees in Matthew 15 rebuked Jesus for letting his disciples ignore their ritual hand-washing, and Jesus shot right back that they were breaking God's law with their tradition of Corban? Odd association, but clearly Jesus was far more concerned about their hypocrisy than he was about their man-made ritual washing requirements. Between that and the OT context, pulling ritual water baptism out of John 3:3-5 seems about the most unlikely conclusion possible.

Bottom line, all this is rather difficult to render in the English. English doesn't have a perfect replica of the dual-use "above/again" construct (at least that I can think of). So we have to pick one or the other and let the potential dual use come out in teaching the passage. As the English idiom "born again" carries both meanings quite well, it is probably a superior translation choice in this case. "Born anew" would be about as good.

Peace,

SR