Having Cypher in fact be one of Agent Smith's infections would be a good way to tie the plot from the first movie to the second and third ones. However, it represents a logical leap in that a part of the matrix program must enter the psyche of the person while he/she is plugged into the matrix and then continue on after that person is disconnected and returns to the "real" world (I put real in quotes since there is some skepticism as to whether the unplugged world is in fact reality). I believe this leap is established in the second movie and is a good explanation for Cypher's deviation in the original matrix.
Whoa there!
First of all, yes, the brothers did always plan this as a trilogy, but so did GL with Star Wars and he radically changed the plot as he went along so whether they had all this planned is unknown.
Secondly, Joe Pantoliano was in negotiations to be in the new films but asked for too much money and lost the part, which he talks quite amusingly about (as opposed to Marcus Chong who pulled guns on people, apparently). He did the Sopranos instead, which he was very good in, but sadly we will miss his neatly cynical presence and whatever means would have been his return, in either of these films
Howz about this -
When Neo defeated the sentinals, it seemed like there were blue sparks...... kinda like an EMP. Smith set off an EMP possibly at the same time during the attempted 'counter strike'. Could it be that the link some how generated an EMP? Or just that the EMP was close enough to affect the machines - Neo and Smith/Bane???
Coincidence? I think not.
There´s something I didn´t understand in the chat between Neo and the Architect. He said that going through the door at Neo´s left (to save Trinity) he woud go back to the Matrix and the whole human king would be condemned. What is the relation between going back to the Matrix and saving Trintiy and the extintion of human kind?