Another great essay on The Matrix Reloaded [in .pdf format] which explains a lot of the themes, images and symbolism of that film.
Of course, all essays of this type very much depend on the outcome of the third film, Matrix Revolutions, to validify some of the author's arguments - but this article goes a fair way without the needing that validation.
It also explains one thing that stuck out in my mind: why there were crows in the background when Neo was brought by Seraph to see The Oracle? (The image that sticks in my mind is Agent Smith walking towards Neo as crows fly out of frame around him). I mean, I've never seen crows gather like that in an urban setting. Pigeons, yes; Crows, no. Crows, I've only seen gather like that in parks - not that I'm suggesting that it's impossible, btw, just that it's unfamiliar to me. But it makes sense as this: the writer suggests that each time Smith appears it foreshadows death of some kind. Symbolically crows imply contention or discord; however, I found an beautiful description of the symbolism of the crow in the Afterword of J. O'Barr's The Crow:
For a hundred thousand years the greatest of the gods was the crow, the dream carrier, who brought civilization to the people in paleolithic times. Mammoth-ivory carvings found over a vast area from Europe to the near East depict a goddess with the raptor traits of a carrion bird: three-fingered talons and a beaked face - a predator crow with breasts.
About ten thousand years ago, when the goddess became a god, the same winged omnivore continued as chief deity almost everywhere: the archaic Greeks called him Cronos - literally the crow - the tireless traveller and hunger machine the Romans renamed Saturn, god of time. The sun god Apollo, whose name means means The Destroyer, was another Greek avatar of the crow, as was the Norse king of the gods, Odin. To the Celts, as well as Aboriginal-American nations, this scavenger bird carried the cosmic signifcance of The Great Benefactor, the creator of the visible world. The Germanic and Siberian tribes similarly worshipped the crow as an oracular healer. And in China, the black-feathered predator was the first of the imperial emblems, representing Yang, the sun, and the vitality of the Emperor.
During Medieval times, "the shadow of the sun" was how European alchemists defined the crow, their symbol for the "nigredo", the blackness of despair and its poison-cure, the unity latent in chaos. That unity is the crow's rapture, a lifeforce so powerful it can actually live off death itself, that - and it's outer space colour in broad daylight - is what impressed the first people. The crow is the hunger of the sky; when it comes down, it eats everything - including the dead - and it rejects nothing. It is invulnerable. It is wider than time...
Therefore it could be said that Smith represents death - as Neo says Smith's attempt to twin/write himself over Neo felt like death - and we know Neo, on some level, represents life. In which case both are intimately connected in very yin-yang way - and quite likely one can't overcome the other. (Well, not without breaking out of their representation, anyway).
Other miscellaneous points:
1. To clarify Neo's comments to The Kid (the one who finds him the minute the Nebuchadnezzar sets down). This story is shown in The Animatrix, where The Kid becomes aware of The Matrix (and Neo) partly through a dream of falling to his death. Finding himself in the circumstances of his dream he does indeed choose to fall to his death and die within the Matrix (there's also another motif of flocking/flying crows here too). It's only after The Kid's death that he awakens in the 'the real world'. Hence Neo says he didn't save The Kid, The Kid saved himself. I think it was referred to (by Trinity) as self-substantiation, or self-actualization - I'm not sure which.
2. If indeed the Oracle is a program then how did she know Neo wasn't sleeping outside of the Matrix? Is there (as many people don't want to believe) a Matrix within a Matrix?
3. What was Morpheus talking about when the Nebucanezzer is destroyed? He states: "I deamed a dream, now that dream is gone..." Superficially describing a man who's dreams/hope is gone which is natural as his belief in the prophecy and the Oracle have been shown to be false. However:
Biblically, Nebuchadnezzar is a king who has puzzling dreams.
And the king said unto them, I have dreamed a dream, and my spirit was troubled to know [what] the dream [meant].
Nebuchadnezzar was also the greatest king of Babylon, reigning from 604 to 561 BC. He restored his country to its former prosperity and importance, and practically rebuilt Babylon.
There's more on Babylon - particularly the captivity of the Jews by (you guessed it), Nebuchadnezzar, in (yes, again) Babylon - but I'm not gonna go into it.
4. Someone else picked this bible ref. up:
When Agent Smith first approaches (but doesn't meet) Neo in the early part of the film the license plate number of the black Audi he pulls up in reads:
The corresponding biblical passage is Isaiah 54:16:
"Behold, I have created the smith that bloweth the coals in the fire, and that bringeth forth an instrument for his work; and I have created the waster to destroy."
5. I always wondered about the leather costuming of characters within the Matrix - it seemed a bit BDSM to me. I pretty much settled on the idea that in a system designed to subjugate that apparel literally became one of bondage (yes, you read that right). But apparently, one of the Wachowski's is/was leaving his wife to marry a dominatrix, or something - I really didn't want to know. So that explains that.
So what does it all mean? I guess we'll have to wait until the third film is released to find out.