While I agree with you that The Matrix really hit the Zeitgeist, I wouldn't call it a bad or even mediocre movie. It's a solid sci-fi cyberpunk action movie.
I personally wish they explored the early part a bit more where Neo is wondering about reality. The action is great, but a contrast with broader discussions behind the meaning of The Matrix would only make the action even more intense. The part about "Neo (The One)" and Trinity's and Morpheus' relationship to the prophecy was really weak though. I thought it sucked even as a late pre-teen.