»Burly brawl is symbolic«

I believe the brawl between Smith and Neo (amazing CGI) is symbolic: It shows neo is vulnerable. This probaly will play a significant part in "Revolution."

This is also shown by Neo's blood when hit by a sword (at Mero's castle)

Is that the referance to Gnostiscism they where talking about?

i wonder why didn't he just destroy Smith as he did before? Hmm to make a show i guess..*sighs* Hollywood..

Because the previous destruction obviously didn't work very well - it gave him all sorts of new powers and abilities.

Lemme think..i can see all the source codes hmm i can control them hmmm why not delete it?

A virus?

All viruses can be deleted after they are found and i don't know if Neo cares damaging matrix by doing so.

I don't believe the Matrix is quite so easy to "re-write."
The easiest thing (the one that almost any "free" person can do) is to re-write the factors involved with your residual self-image. Increase your speed, endurance, etc. Neo has got that down to the point of changing his own code's gravity. Affecting others is probably very tricky, as evidenced by what happened when Neo tried to rewrite an A.I. code. He probably used his knowledge of programming from his human hacker life, and it just wasn't adequate when it came to such futuristic programming.
"Jumping-In" Agent Smith is being protrayed as a necessary, but ultimately rash decision. Obviously, Neo is not all-powerful as some fan-boys wish.

I believe the correct spelling is "fanboi."

I think you're right about his not being able to really control other programs codes to the point of omnipotence. But he can control the "non-sentient" programs (like bullets and the sais that he pulled off the walls in the Tibetan palace fight) because they have no self-control or don't have as advanced a code, which explains why he can't just freeze the agents, twins, or vampires in their tracks.

It has been noted that Neo is referred to in a few instances as being ......" STILL ONLY HUMAN". Does anyone think that there is something more to this?

This "human" talk has been pulled over the eyes of some posters to blind them from the truth: That Neo is "human" just as Persephone is human. But deep inside he is alsoa software