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I am not an expert on all religious/philosophic terms, but I think that you can see different symbolic figures in many of the main characters...
Christianity:
Deus Ex Machina aka the Source is God.
The Architect is Satan and the agents are his demons (demons can possess human beings, which is exactly what the agents do).
The Architect, altough dressed in white, could very well be seen as Satan. He tries to stop humanity in it's path back to God. He wants Neo to re-integrate himself with the Matrix, so that a new cycle can begin and no spiritual progress is made.
The reason why he is dressed in white is not so important. Satan can appear as deceiving and not 'scary' at all.
Neo chooses the 'wrong' door, so he neglects Satan's seduction like Jezus did.
Later on, Neo goes to the Macine City. In the Real World he is seen as a real human that wants to restore his relationship with God (Deus Ex).
In the Matrix, Neo is Jezus. He sacrifizes himself and he takes away all the sin (the Smiths) from the world.
Smith is not the devil, but he is a bastard that spawned from the devil. The Architect, as Satan, originally was responsible for the agents (his demons). One of his demons, Smith, was so full of hate that he managed to spread more and more sins among the world. Near the end of M3 the entire world seems to be 'polluted' by sin. The only one who can take away all these sins is Neo (Jezus), the saviour.
If you see Smith as a 'big demon' and as a sinner, you might also view him as the Anti Christ.
The Oracle is simply the Oracle; a person that is a medium between humans and God and whom can guide you in the way back to God, which was exactly what she did.
The Merovingian and Persephone are Adam and Eve. They were one of the first AI-programs that discovered senses, feelings and human sin. For this they were punished and banned into the Matrix.
Buddism:
Buddism is all about re-incarnation. When someone doesn't complete his purpose on earth, he has to return in another lifeform: reincarnation.
That's exactly what happened to the One: Neo is his sixth incarnation.
In Buddism there is no real God. God is the energy among us. God is Deus Ex Machina, because he is the centre of all the energy involving the Matrix and the machine-world.
Buddism is also about enlightment. Enlightment is to become free from all the materialistic things on this earth.
The rule of Karma is also important. This rule implies that the things that you do, say or think in your life will bounce right back at ya. If you give love to someone, love will be given back to you; if you hurt someone, you will be hurt back. This doesn't have to happen in your current life; it can happen in your next life.
The rule of Karma brings in the yin-yang principle: positive versus negative. Everything is in balance and balance is what the Matrix is seeking.
The Architect and the Oracle are a perfect yin-yang-pair.
The Architect is maintaining the rules of Karma. He tries to keep the Matrix in balance and he wants to avoid that people achieve enlightment. Enlightment is equal to freeing your mind and leaving for Zion where they will live less materialisticly (more sober and 'poverty' in Zion).
So the Architect can be seen as negative energy, which produces mathematical engrams in order to keep the people running around in a cause-and-effect-circle. Neo is the first One who breaks free from the rules of Karma. Neo enlights himself when he chooses the 'wrong' door at the Architect. His next step will be reaching Nirvana, but more about that later...
After Neo's enlightment, he is more aware of the energies around him. A true budha can mentally leave the materialistic world behind and litterally feel the spiritual energies around him. That's why Neo feels the Sentinels and can even manipulate them.
Neo and Smith are also a yin-yang-pair.
Only they are one person. Almost every human being on this earth has a darkside. Smith is Neo's darkside. The most important step to enlightment/nirvana is dealing with your darkside. When you deal with a problem, it is important that you can determine and 'get to know' this problem first.
That's exactly what Neo is doing. He is fighting himself! He is fighting his darkside in order to get to know it better. It's like Seraph said: you don't know someone untill you fight them.
Budism is also about soulmates. Two seperate souls that were once as a whole. One of the goals in life is to find your soulmate and step into Nirvana together.
Neo found his soulmate, Trinity, in his sixth incarnated life.
Now in order to reach Nirvana, you have to leave everything behind on earth without carring about it. Trinity did! When se died in the ship, she was at piece with it.
Neo was not at peace with it yet, but after the fight with Smith he realized it. He was greeving and full of anger about Trinity, but after the fight he realized that the only way to join her was to step into Nirvana too. He left everything behind without carring about it. He had piece with Trinity's death, so he would have piece with his own death.
He sacrifized himself. With this he also killed Smith, because Smith is part of Neo; his darkside. There can be no light without dark, so they both disappear.
Your darkside is often related to materilastic stuff, like money and power. Neo literally said 'fuck you' to this side of himself and this is why he stepped into Nirvana.
What is the Merovingian in buddism? I think also a negative energy form, a cause-and-effect-engram that wants to stop you from breaking free from the rules of karma. This is why he bothered Neo twice.
In Mobil Ave we somewhat witness a re-incarnation process.
What we see in Mobil Ave is Neo's soul trying to get back to his body in order to start a 'new' life. When he returns to his body, he is indeed 'renewed'. He now understands and has compassion for the programs too, thanks to his dialogue with the program family.
So in fact Neo has begun with his seventh incarnation, although his last reincarnation was 'speeded up'. In his seventh life the One finally completes his true purpose on earth and then goes and rest in his Nirvana-state.
Alternative Christianity:
If we look at the Matrix as a closed dimension, as our world, then there is another symbolic possibility...
The Architect is God, sitting on his throne, reviewing Neo's life on the monitors.
The agents are God's angels that try to prevent people from waking up and going to hell, which is Zion. Because it is deeply underground and dirty, Zion could be considered as hell. Humans give in to their animal instincts down there (the erotic dance) and they suffer from the passing of time. They will die down there and when they do it's a definitive death.
The Matrix is (middle)earth where life and death, light and dark, instinct and divinity, materialism and spiritualism exist together. It is the middle-lane between heaven and hell, where heaven is the machine-world.
Programs who hate the static perfection of the 'heavenly' machine-world can escape to the Matrix, where they are considered as exiles. Humans that don't believe in God (Architect) and his created world are considered as true sinners and they are exiled to hell: Zion.
Now if you do a bit of assuming, you can see Smith as Lucifer. He was once working as an angel for God (Architect), but then turned against him and took 1/3 of the angels with him to earth. The only difference is that Smith creates his own army of 'anti-angels'.
But this doesn't have to be neccesary. That's the brilliance of the Matrix, different symbolics are possible at the same time.
The Merovingian can also be seen as Lucifer, who turned against God and took 1/3 of the angels (the other rogue programs that protect him) with him to earth (the Matrix). He can also be seen as Adam, who likes to explore the senses of sin.
Neo's different roles:
In M1 Neo is mostly a beginning buddhist, who tries to free his mind and break free from the rules of Karma.
In M2 Neo could be seen as an advanced buddhist or as Loki the serpent aka Satan. God (the Architect) put Loki (the Devil) inside the garden of Eden (the Matrix).
Loki wants to break free from the perfection of the garden and he opposes against God. This is exactly what Neo does: at the Architect's room he really leaves the perfect garden of Eden and he denies the Architect (God).
I got this part from a brilliant set of essays, which you can find here:
wylfing.net...
I really would advise you to read them if you have the time, they are very-very good.
In M3 Neo's digital-self went to Mobil <--> Jezus' soul went to Limbo
Trinity went to club Hel <--> Jezus' body went to hell.
When you see Neo and Trinity as one whole (because they are soulmates), then Neo is the soul and Trinity is the body of Christ.
When Neo leaves Limbo, he has learned to have compassion for the programs/machines and he becomes a true saviour for both worlds. So in M3 he is truly Jezus.
Creation of earth:
God created the world in seven days. On the seventh day he rested and took a walk in the garden.
If you see the Architect and the Oracle as a yin-yang-pair, then they both represent a half-god and together they are God.
It took Neo seven lifes in order to achieve a 'perfect' world which equals the seven days of creation.
Both the Architect and the Oracle take a walk in the park at the end which can be seen as walking in the garden. Together they are God and after seven days/instances, they have finalized the world.
Let me know what you think 
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