I disagree with that read of the evidence they list, to wit: > In the introduction to a copy of the Final Shooting Script included in the book, editor Spencer

I disagree with that read of the evidence they list, to wit: > In the introduction to a copy of the Final Shooting Script included in the book, editor Spencer Lamm notes that “everything” in the script was filmed but “changes occurred during editing.”[...]the part “where Cypher tells Neo there were five potential Ones before him was shot and then cut in postproduction for reasons only [Lana] and [Lilly] know.” So the quotes here say they shot everything in the script, but then they made changes in the editing room for reasons only known to the writers of the trilogy. It could be for runtime! I don't think there's any definitive evidence it isn't, but clearly this account also supports them shooting something that they later realized would screw up their planned script. I also wanna say that there is an ambiguity over if the five "ones" are actually Ones or just people Morpheus believed are ones. It wouldn't contradict the later plotline of Neo being the sixth One for Morpheus to mistakenly free five people who aren't Ones and get them killed - but it would be really confusing! Since the people in question are summarizing a deleted plot arc that the directors removed, I suspect they may be summarizing in a way that wasn't accurate to the understanding of those directors. All of which is to say that the blog article is telling a very specific story about what seems like pretty ambiguous evidence. The script had reference to previous people pulled out as potential Ones having died to agents. It would be confusing to the audience for these to be five "fake" ones and then also have five previous real Ones, but it wouldn't be internally contradictory. The only way it directly contradicts is with a very narrow meaning which I don't think the blog post convinced me was intended. Beyond that - as I said above - since they never put it into the movie I think this could count as "being intended from the beginning" where the beginning is the release of the first movie.