Much like the Star Wars and Harry Potter franchises, the extent to which Everything Was Carefully Planned In Advance has been greatly exaggerated. It's just not possible to think that far ahead!
Like, shooting and then deleting a scene that you think might hurt the plot in future movies is "carefully planning in advance."
I disagree with the article’s premise that it would have changed the story of the sequels - but they make a good case for it being cut for incidental reasons.
> 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.
This of course ended terribly in Episode 8 when Johnson single-handedly destroyed everything Abrams had put in place and left him nothing to go on for the finale.
Even the Star Wars expanded universe was carefully and competently taken care of prior the acquisition - so many books and yet so little inconsistencies. Then Disney decided to throw all of the decades of worldbuilding away for three shitty plots and an endless lot of Rey-based Rule 34 material.
The Star Trek reboot quality is similarly questionable, but at least they didn't simply go ahead and un-canon all existing works.
Good on ya to point out the silver lining.
ETA: not to mention, the "character dies and gets reborn" plot was already questionable in TCW (where Darth Maul was revealed to have survived being sliced in half by Qui-Gon Jinn in Episode 1), but that one at least had a decent bit of usage... Palpatine's appearance was mostly the reveal at the end on Exegol, a fight and his (hopefully final...) death.
The only way I can see any future films being set is somewhere between the trilogies (there's more than enough to be explained between EP3/4 or between 6/7) or an alternative-timeline reboot happening after EP6 (or maaaaybe but difficult given the deaths of primary actors, a timeline split caused by the destruction of that superlaser planet).
(Seriously, time travel as a concept is annoying, especially when everyone uses their own version of how it works!)
All symptoms of staggering mismanagement by Disney, of course. A trilogy with a stupid planned plot arc would have been better than the sequence of "solid but uninspired Star Wars throwback" + "interesting and out there reinterpretation of the mythos" + "but what if RotJ again but dumber?"