I enjoyed Reloaded and Revolutions, but there is one way they fall short of the original and it has to do with their structure. R&R are philosophically dense, even more so than the first, but the philosophy just kind of... exists apart from the story. In the first Matrix, most of the philosophical dialogue drives the plot or the characters' motivations in a critical way. Either you learn something valuable that develops the characters, or the conversation sets something into motion. In R&R, there are many scenes where the characters sit around and say things that sound cool, but 99% of the dialogue has no significance. They'll occasionally drop a clue or explanation for a future event, but most of the scene is philosophy for its own sake. The plot either happens independently of the conversation and interrupts it or the conversation ends and the movie continues from there.
I guess you could say the sequels take the scenic route. The Merovingian encounter is a good example, but I'll admit it's still entertaining.
