I have two guesses:
1. The Ws didn't want to do sequels and the studios basically had other people ghost-write and direct them but still put the bros name on it (which is what they sequels FEEL like)
2. The Ws basically spent 10 years developing "The Matrix," slowly adding things to the mix, talking it out, "borrowing" from other sources, and just having fun creating this world they never actually expected to go anywhere. Then, when faced with having to do 2 more movies in 3 years, they just didn't have it in them; the first film basically exhausted all their creative inspiration and contained all their favorite "homages" where their true creativity came from.
I'm sure the first "conspiracy theory" is unlikely, but when you watch the first film it just feels so much like it was made by someone entirely different; none of the creative or stylistic genius of the first film is present in the sequels; it really is like someone else tried to capture the look at feel of The Matrix and turn it into a franchise without any true understanding of what made the original so great.
Then again, that's what Lucas did when he made HIS sequels (i.e. prequels). But then again, I think a lot of people now realize that Lucas' help (his producer Gary Kurtz, director Irvin Kershner) had a large role in crafting the early movies. Was there anyone with a big hand in "The Matrix" that was missing from the sequels?