I haven't seen the second one, it seems like a lot of fun.
I do have to agree that the third one was really confusing, but it's the one that I like the most!
The whole 'human headquarters' getting attacked by a bazillion of those computerized flying squids, plus Neo gets super cool powers when he gets blinded.
Even if I did understand most of it, I'm wondering how the Chinese guy and the Middle Eastern girl survived at the end.