JediHDM
Jedi of the Matrix
Starting with Bane not looking like smith, the program is designed that the residual self image is loaded into the Matrix. Smith infected Bane's residual self image, effectively killing Bane's mind and replacing it with himself, but in the Matrix, Bane WAS Smith. When Smith picked up the phone, he was uploaded into Bane, but he wasn't uploaded AS Bane. As for why the Agents cannot move through Zion, it is because they do not have a body to be loaded into. The equivalent of an agent, in Zion, is a Sentinel. The Sentinels, at the same time that Agents are trying to learn the codes to the Zion mainframe, are searching for the location of Zion. If Zion were not another program, another method of control, it wouldn't matter how much of Neo had been rewritten by Smith. If your mind is infected by a program, it may enhance his abilities in the Matrix, but it would be unable to allow him to stop four Sentinels in the real world. As for the code, Neo couldn't see the code of the Matrix until after he had thrown all pre-concieved notions about the Matrix out the window, and had become the one. Maybe, the problem is not Neo being the One in the Matrix. Maybe the problem is that no one else has realized that the One must be the One in everything he touches, and that no one has been able, thus far, to make his mind believe that the machines may have thought more in depth than realized.
Have you ever heard of "Situational awareness"? it is crucial to the longevity of fighter pilots, as it allows them to know, more or less, where everyone is at the same time. This, coupled with the Neo/Smith fight scene, is the strongest evidence i can think of right now, that neo can feel his opponents. When Neo is fighting Smith, He knows exactly where to punch, kick, jump, hit with rod, etc. If he were reading the code of Smith, he would have to look at all of them, to know what each was going to do. How does Neo look at the doors right as Smith runs through them? He feels them coming. Neo does not have to read the code to knowwhat is happening. Real-world ex. When you meet someone, assuming of course that you do meet people, do you read their code to find out what kind of person they are? No, you do not. You have to feel them out, get to know them. The same is true with Neo. Just because Neo looks at the code before talking to the Merovingian does not prove that he reads the code of everything he encounters.
<oracle telling some guy about how she had to tell neo somin she was not ment to. this made him realise somthing to help develop powers outside the matrix.>
As for this, this is more evidence for Zion being a program. What powers does Neo have, that are not connected to a program? none. Therefore it logically follows that, if neo is to develop powers outside the Matrix, then whatever 'outside the matrix' is must be another program.
If you go and read 'Revolutions Predictions', i explain my theory for a duality of programs at length. As always, if you have any objections, post 'em.