The Matrix's sequels do have a lot in common with the SW prequels—they are boring, have way too much CGI, and are ultimately pointless.
I don't think The Matrix was ever intended to be anything other than a standalone movie at first. If you read the script, some interesting backstory is presented: prior to finding Neo, Morpheus had taken in five other people whom he was equally, fanatically convinced were the One, and all five of them died fighting Agents of the system. (This seemingly unjustifiable conviction led even more weight to Cypher's betrayal of the team.) Ultimately, this information was not included in the final film, and in the sequels the idea of Neo's "five predecessors" was instead changed to there having been five Ones before him who reset the system to save humanity. The effect of this was to reduce the idea of the One to a mere pawn of the machines, rather than someone who got sucked into Morpheus' seeming delusions but ultimately turned out to be real.
Since this unused backstory was what the Wachowskis had in mind while making the first film, we can easily see that the plot of the sequels has little resemblance to their earlier ideas. And since it was the first film that audiences identified with rather than the sequels, the situation is again analogous to the SW prequels, whose changes to the continuity and the deleterious effects this had on quality are well documented.