So of course I saw Matrix: Reloaded today and I'm trying to work out exactly what it was that bothered me about it. I don't plan to include any spoilers but if you'd like to see it with a clear mind, you don't have to read this.
I think what made the first Matrix so compelling was the mysterious way in which several layers of complexity were unfolded. As Neo's world falls apart and the new, "real" one is constructed, we're given just enough detail to fuel allegorical and philosophical speculation that boggles the mind. The story references such a wide range of ideas that the possibilities seem endless and therein lies the excitement.
As far as I can tell, this is exactly what I was missing in the sequel. It would have been easy to overlook the other shortcomings (just remembering the Zion scenes makes me cringe) if the film had been charged with the same kind of complexity as the first, but it just falls flat in that department. I'm beginning to wonder whether the ideas that I so loved are just playthings for the brothers Wachowski, thrown in as necessary to attract a certain crowd, much like action scenes. Perhaps this is the nature of the beast with the second part of a trilogy (it does do a good job of giving you enough information to sufficiently set up the third part). I will postpone final judgment until November, when Matrix: Revolutions is released.
And yes, the fight scenes are cool, although sometimes unnecessarily long and failing to advance the plot or develop the characters.
Additional reading: Adam Gopnik's "The Unreal Thing", a decent critique that's smug and condescending in that characteristic New Yorker way.