Second part was far better. Third part was simply one big beating-up without any morals, with the screwed up ending which burried every piece of sense of this movie, and replaced with neo-gnostical para-religious happy end.
Let's face it, third part lacks the perfect dialogues, lacks the perfect Oracle character (the actress died, sadly) and generally beside good special effects it's not really well done - and special effects aren't what I've came to the cinema for.
Compare second part - there were excellent scenes (the scene with Neo fighting with Smiths is far better than the Neo/Smith fight at the end, or even Neo fighting with Seraph is excellent), there are excellent dialogues (the Oracle, the Architect) and generally well done moments (the chase through the highway).
Matrix 3 should be rather called "Matrix: Apocalypse". 3 hours of watching as robots are fighting with people, with their totally physically impossible mechs which can move two arms in different directions, looking like from some bad old children anime toon and the dull ending about "peace between humans and machines".