Reading the scenes, I don't see these as being incompatible with the overall plot line.
The story presented here is that there were five previous "Ones" and they all faced an agent and were killed. But, if you recall, that's exactly what happens with Neo. His death at the hands of an agent is exactly what "unlocks" his powers. There would need to a be a couple more dialogues in the sequels but it would be trivial to address what happened to the other five after they were "killed".
So while it may be true that there was no master plan for the sequels (and I have absolutely no doubt they came out very different than originally envisioned - that's the creative process), I don't necessarily see this as strong evidence of that fact.
It was probably cut because the subplot just adds complexity for the audience without really adding much to the story.
I agree. No evidence was presented to support the sequels were "mostly the result of retroactive revision and was never planned when the first film came out." Revision already take place in all creative storytelling. Also where does he come up with the idea that the perception is the films were "mapped out in advance and executed in accordance with a foolproof master plan?" Seems a bit extreme.
All stories are a creative process and small and large details can change as a story continues.
For instance, originally machines used human brains as part of a greater neural net within the matrix. But then executives forced the Wachowskis to change that idea into humans-as-batteries to make it more palatable. So they re-write portions of the arc to fit that new narrative.
So all I see here is the "5 predecessors" plot removed from the first movie becoming 5 predecessors in the "matrix is a lie" plot, which may not have changed much. It's silly to speculate without just asking The Wachowskis directly.
> When I watched the first film I just assumed that Morpheus had found others and been wrong about them…
I'm pretty sure it's even hinted in the film how Morpheus had thought Trinity was the One until the Oracle had told her that she wasn't - but that she would fall in love with the One.
And they pulled some of that into 2/3. The oracle is another form of control. She even told Neo he was not the 'one', and I suspect said the same to the others. Until he stopped believing their lies he could not be the 'one'. But he needed a push, the love for Trinity. So the oracle set that up. Another form of control.
The story presented here is that there were five previous "Ones" and they all faced an agent and were killed. But, if you recall, that's exactly what happens with Neo. His death at the hands of an agent is exactly what "unlocks" his powers. There would need to a be a couple more dialogues in the sequels but it would be trivial to address what happened to the other five after they were "killed".
So while it may be true that there was no master plan for the sequels (and I have absolutely no doubt they came out very different than originally envisioned - that's the creative process), I don't necessarily see this as strong evidence of that fact.
It was probably cut because the subplot just adds complexity for the audience without really adding much to the story.