OK My take on it..... this is gonna be llllllllooooooooonnnnnnnnnnnngggggggg... Bear with me....
Yeah there were bible references, and yes Satan is French... are you suprised?? I am not
but that's not what struck me... What made it clear for me was the Architect...
Look at it from a software/system design standpoint. Programmers will get this...
Remember the matrix only exists to to keep humans alive to produce energy. Energy for what?? to keep the matrix going? pointless... There is a mainframe we have been told that but, in Reloaded they never get to it...
Neo is a bug in the Matrix, there were 5 previous versions with 5 bugs, Neo is the sixth in the sixth version.. The room where the Arctitecht exists is a system outside the Matrix. It's in a middleware/messaging system between the Matrix and the Mainframe. The entire interaction between the Architect and Neo was a Debug session. The Architect told Neo that there would be a new version, and he had to proceed to the mainframe and give it the anomolie in order for the new version to be reloaded, if he did not everyone would die.. The Architect Lied!! He needed to trap the error in order to fix it . Neo dind't accept the parameter. No one would die if he went back into the Matrix, if Neo returned there would be no debug, no hotfix and no new version. The architect couldn't very well trash the old version without a new one otherwise everyone would die, then they would have no power. So he lied.. Neo didn't take the bait... You'll notice the world did not end when he went back. He didn't lie about Trinity, she did die... Neo just brought her back..
The Oracle is also a debug routine.. she handles things differently, she interacts with Neo in order to debug him. She also LIES! remember in the first movie she said he wasn't the One... Why would she tell him that it was either a Lie or she doesn't know as much as she lets on. She was right that Neo's road ended at the door to the main frame, and if he had gone through that door of the architects little room it would have but, he didn't.
Ok so what about Zion?? I get the imperssion Zion is a system on the outside of this middle system behind a Firewall or exists in a DMZ outside of this middleware system. Why else would the Sentinals keep on digging after they attacked Zion?? Where are they going??? The people in Zion access the matrix via this middle system that has been hacked and protected via this DMZ/Firewall. Why don't the people of Zion realize this?? I dunno maybe the system in which they exist and is hooked to the firewall/DMZis also a matrix (anti-matrix???) The Arcitect refers to destroing Zion, and if fact maybe they did destroy the connection to it and as far as he is concerned that would destroy Zion.. then again he could be LYING!!
So the folks from Zion don't realize they are in yet another system, however in the end Neo does realize this, and realizes that it operates under the same priciples and rules and is able to stop the sentenals. The other ship didn't do it, the ships need to be shut down in order to do an EMP. Why the comma?? dunno maybe it takes more to stop the programs in the middle system, maybe the realization of this put him in tyhe coma. Remember he blacked out in the first one when he found out about The Matrix.
What's with Agent Smith?? Well he is still a program, however he is a rouge and apperently has some of Neo's code. Rouge programs we are told do exist in the mtarix and are ghost, vampires, and whatnot. However like all of the other programs in the Matrix outside of the French Satan, The oracle, and the Key maker he has very little knowledge of systems outside the matrix. In the first movie we know he knows an outside exists and wants to get there but, Why? He also has a need to get into Zion in order to do this. At the end of the last Matrix he is already pretty much a rouge program. So his motivation is the same is Neo, get out of the Matrix and and be FREE and maybe take control of the Main frame. At this point though he is not very bright, If he was he would have realized he is capable of the same things as Neo. All 100 of him could have taken off after Neo when he flew away. So he is still bound and ruled by the contructs of the Matrix.
What about the other smith?? Yeah the guy that gets copied and into Zion?? Simple same Smith different copy but he is connected to Neo as well and Neo connected to him. What bugged me was what was with the ZionSmith cutting his hand making it Bleed and then shaking Neo's hand?? Was the Blood another Code exchange perhaps?
This could explain why Zionsmith survives the sentinals and is also in a comma, he and Neo are linked by common code and common purpose. I think in revolutions you will see Neo and Smith become one unit...
Ok there is more but this is long enough....
Oh yeah, except this... I thought the Primal / Rave bit was way too long and seemed out of place too.. I think that is just window dressing to spice up Trnity and Neo getting it on...