My take is that if you thought it was some philosophical story, you're a fool. The blatant holes that were rampant in the first one should have clued you to that. The second movie hinted that maybe things weren't so silly by posing some questions, and the third completely failed to answer ANY of those questions.
I loved the first one, I thought the second one was a fantastic action movie, and I thought the third one utterly failed no matter what you were looking for. The story was totally stupid "You're crazy! NO-body can [insert difficult feat such as skiing a difficult mountain, beating a champion fighter, piloting through a difficult course]", the action was beyond boring ("I punch you but cannot hurt you. Hmm, maybe a few more minutes of punching will change something"), and the acting was horrible, even for a sci-fi movie. Take away the good music, the creative camerawork, and any feelings I had for any character, and I'm left with the impression that the first matrix was worth two tickets and I'm now paid up.
The really sad thing is that these guys cost themselves a billion dollars or more by making a horrible movie. They had the chance to found a franchise on the scale of Star Wars and they failed miserably. Imagine if Return of the Jedi had ended with Luke and Darth Vader shaking hands and agreeing to disagree, do you think there would now be dozens of video games, countless novels, 3 more movies, an entire subsection of the toy industry?