The deleted bits (the conversation between Neo and Cypher, and the followup conversation between Neo and Morpheus) doesn't contradict the sequels. They simply show that Morpheus was wrong about who the One was. The existence of the failed candidates doesn't contradict the existence of the failed predecessors. If anything, it fits into the numerology of the trilogy (6 candidates, 6 Ones, 6 crew members, 6 ships, 6 trips into the Matrix, 6 Zions, etc.)
Of course the Matrix Trilogy wasn't fully written out when they made the first film. The Wachowskis never claimed that. They said it was all conceived as one whole, and the specific execution of that concept (i.e., the screenplays) changed after the first film to reflect the narrative that actually made the final cut in the first movie... Which is exactly how things work in Hollywood, because canon is only what actually makes it onto the screen.
Yeah I totally agree - as much as I would have liked these scenes in the movie because they do really flesh out Cyphers motivation (and its not like the Matrix was an excessively long movie to begin with) I dont think these are incompatible at all.
That being said as much as the second two films get shit on I rewatched both recently and number 2 really is quite good - not as iconic as the first Matrix but still solid. Unfortunately it seems its reputation got really spoiled by the third movie which.......well we all know how that goes.
The third movie is the best sequel...when viewed through the understanding that it is a war movie. At any rate, the stuff that happens in the third movie matters, unlike the countless pointless fights between immortal characters in the second movie.
Of course the Matrix Trilogy wasn't fully written out when they made the first film. The Wachowskis never claimed that. They said it was all conceived as one whole, and the specific execution of that concept (i.e., the screenplays) changed after the first film to reflect the narrative that actually made the final cut in the first movie... Which is exactly how things work in Hollywood, because canon is only what actually makes it onto the screen.