I think the Aeon card is a difficult card, perhaps the most difficult of the Thoth deck. It presents a doctrine, which is a take-it-or-leave-it proposition, that something like history or reality goes through measured and meaningful periodic change - in the case of the Aeon, that a massive and inexorable spiritual change happens to humanity roughly every 2000 years, and that this is connected in some way to the precession of the Vernal Equinox (0 degrees tropical Aries).
If you don't believe any of this, how can the Aeon card make any sense?
Crowley believed it, Theosophists and many who believe an "Axial age" and other ways of "meta"-interpreting history believe it, but I don't. But just because I don't think the idea represents empirical fact, doesn't mean it doesn't mean anything. It obviously comes from somewhere, and reveals the thoughts of the creators of the idea. Thus, by studying what they meant, we may come to an understanding that goes beyond how they expressed their explanation of history (which I consider largely wrong), and arrive at something truer.
That is, to use Crowleyan-Hermetic terminology (from the first line of the Emerald Tablet), they were wrong about the "true" and the "certain without error", but what they wrote was very much "of all truth". That is, what the Aeon expresses, and what the belief in the spiritual meaning of the precession of Equinoxes expresses, what Crowley had Harris paint and the doctrine it illustrates, is timelessly and infallibly true.
The Aeon has many similarities with the old Judgment cards, and Crowley was well read in Christianity (I personally see Crowleyan Thelema as a kind of Christian Tantrism, or Left-hand-path Christianity). So, without going into the technical doctrines of Thelema that informed the design, it is perhaps good to compare the intentions first, with the aim of getting to the "of all truth" part, rather than dwelling on the dogmatic aspects, which could be erroneous (the "truth" in the limited sense).
Both the old card and the Aeon are about rebirth. In the one an Angel blows a trumpet from above, while in the new card a babe emerges in silence from the background. This babe is the New Aeon, which has not yet found its voice; in the old card, the reborn bodies are rising to an unknown judgment. The new card emphasizes the silence of the reborn; the old card emphasized the sound of the trumpet waking them up.
I don't find the old card negative in any way, in itself, since there is no implication of damnation in it. All of the rising bodies seem to be headed to paradise; this tarot card is very different from the scenes of the Final Judgment in Churches of the epoch, where there is a right side and a left side, with one going to heaven and the other to hell. In the tarot card, everybody could well go to heaven. Hell has already been passed anyway, 5 or 6 cards back. I think this implication of the inevitability of the upward progression is reflected in the new Aeon card.
The silence of the Aeon is the great difference between the meaning of the old card and the new one; but we all know that Horus is a war god, a hawk, and that as Crowley expected the New Aeon has been initiated according to his character. War is not quiet, which is why the child Harpocrates is ethereal, and silent. This baby aspect of Horus has yet to grow up, to be fully born; he is spirit, an idea, crying to be heard here and there, but not yet enthroned as his old self, Horus, still is in the background.
In this card, Horus takes the place of Christ in the Judgment seat, and the ethereal, silent child Harpocrates takes the place of the resurrecting figures in the old cards. We are Harpocrates, the children of the New Aeon, written still like a figure in water on the blazing plate of Horus' fire and war. We have been called out of the old, by the noise of his war, the old trumpet of Judgment, but we are still unsure what we will say when we gain flesh and sit in our turn upon the throne.
It lies to us, and all living people, to interpret older expressions into something meaningful for ourselves and our contemporaries. This is what Crowley did with the old Judgment card when he created the Aeon.
(I will forego the points about Christian doctrines about the end-times and the final Judgment being superceded or demolished; they too mean something, and by no means did they have a monolithic meaning to all of the hundreds of millions of people who lived between the first century and the 20th. Many of them saw the teaching of the "Last Judgment" as a realized eschatology - something that could happen in the here and now. They were the mystics, perhaps some of the great (even orthodox) theologians, some Gnostics, and others. They did not see time as linear, but cyclical or holistic, or even dual (an illusion of change in a sea of infinity, with no beginning or end). Christian thought lends itself to mystical interpretations, which is why there have always been so many "heresies" within it. The institutional churches are the tree, and the heresies are the leaves that sprout and grow and fall every season. The trunk preserves the structure, but the leaves are the reason for its existence. It is all-too-often a fine line between a saint and a heretic, and when you study this kind of history unbiasedly, you realize how frequently one could have been the other, if only some part of the context had been different.