I finally figured out why the sequels to The Matrix were so disappointing. It is because, in those movies, the Wachowski brothers tried to continue the series by exploring the metaphysical and epistemological implications of The Matrix, with subplots of boring old war and impossible moral dilemmas. Instead, they should have focused on the moral implications of The Matrix itself.
In particular, they should have expanded on the conflict within Cypher that lead him to betray Morpheus in the first film, the fact that he would prefer to be back in The Matrix than outside it. This could have been done by having Neo reveal to the population of The Matrix the truth (which the end of the first film implied that he would do), and have that as the basis for a conflict among those inhabitants. There would have been those who wanted to fight the machines, leave The Matrix, and try to rebuild the world from its poisoned state, certainly a daunting task, and those who wanted to remain slaves to the Machines, but leave a normal and happy (if virtual) life.