I did not see the connection when I saw the Matrix (more than once), and I consider myself VERY intelligent (like, scary smart). But as an atheist I try to think as little of the bible as possible, so that may be the explanation.
There is also the chance it was unintentional or coincidence. These are not the same thing. The author could have unintentionally used the Jesus story because it was in his subconscious. Or that could have had no effect and these comparisons are all pure coincidence.
Anyway, if you "boil down" the different kind of plot elements that can be in a story, there are not all that many. Betrayal. Temptation. Vindication. Etc. My point being that finding a biblical allegory in any work of fiction might be akin to a guide to astrological signs accurately describing you... I mean, EACH sign is always described with some vague positive stuff and negative stuff that EVERYONE sees in themselves to some degree, so they all sound true. Correlation without causation.
Similarly, if the story of Jesus had a lot of the classic stock elements of a good "hero" story, then you would naturally expect that many, most, perhaps even all good hero stories seem to be a Christ allegory... Correlation without causation. Let me test this theory by picking a random "hero" besides Jesus or Neo: Superman.
Hmmm... Okay, first off Superman was not born of a human woman (like Jesus and the Virgin birth). When not saving the world, he is meek and mild as Clark Kent, which plays into Jesus favoring meekness (saying the meek shall inherit the earth). Ummm... They both have x-ray vision, right? (I'm reaching here.) Okay, so maybe it is not so easy to find a Jesus allegory with every hero, or maybe I just don't know Superman well enough.
Regardless, I WILL say that even if Matrix 1 was a Jesus allegory, there is no reason that Matrix 2 or 3 must continue a biblical allegory. Because the allegory was brought to a satisfying conclusion, the writers to me now seem free to go in an entirely different direction.
Oh, last point: If it WAS a Jesus allegory, then "god" would be...who? I suppose the same being who gives the Oracle visions, huh? But not literally god, rather some being that could be introduced in the next movie or two... Maybe a computer subroutine added by a brilliant human back right when the human/computer war began, to try to work from within to save humans, such as by giving slight nudges here and there to help breed humans who can see through the matrix (i.e., Neo), and communicating with the rest of the "enlightened" humans through a chosen human (the Oracle).
If it were my story, and this is all just off the top of my head, the master computer would analyze what has happened that lead to the defeat of its minions in the first movie and will on reflection recognize that there must be a "traitor" in its own midst, so to speak, the pro-human subroutine (which we'll call Max). The master computer starts a systematic purge process which forces Max to move itself into the Matrix, where it takes human form. But in this place and form, it is vulnerable, and Neo must protect it and guide it to a place where it can re-enter the Matrix when the purge is complete.
But Max suggests the alternative that there is one connection between the main brain of the master computer and the Matrix where, if Max can reach that connection, Max could conceivably gain control of the master computer brain and set all humanity free.
It turns out, though, Max does not want to return. The decades of watching and trying to protect and free humans have given Max a love of humanity where he himself desires to be human (classic Pinocchio character) and in the Matrix he finds himself experiencing life as a human would and thinking he might even prefer to live forever in the Matrix rather than leave and merely watch humanity. So he is waffling on which side he is really on. And we feel bad for Max because he (she?) will be drawn as a sympathetic character.
Well, Neo leads Max through various obstacles, agents, etc. , with lots of cool effects and explosions. At the end, they get to the master computer connector node, only to find that the master computer has been expecting them and wanting them to come to it. None of the master computer's minions were able to defeat Neo, so it knew it had to do it itself. It knew that Neo could not harm it from inside the Matrix, nor could Neo himself use the node to get "into" the master computer since he was, after all, human and not a computer program. It also knew all about Max and, in fact, had added a monitoring subroutine to Max and, once they get into the node room, the master computer triggers that subroutine which further stops Max from entering the node.
But as the master computer pummels Neo, he realizes that while he cannot affect the computer, it's program not being in the Matrix, Max still IS in the Matrix, so Neo can delete the subroutine in Max that is holding him/her still. But the master computer sees this and sets in place a deletion routine that the node that will destroy the subroutine upon entry. Neo realizes that there is one solution. He absorbs Max into himself, thereby becoming part computer subroutine, so that the merged entity can enter the node. The Neo part keeps it from being deleted and it is able to battle and destroy the mastercomputer from the inside.
On reflection maybe that is all to similar to Tron. Dammit.
~psychoblast~
