The main problem with this movie is that it doesn't really tell a story. Nothing is ever explained, and it jumps from one scene to another without any explanation. There is no exposition; only dialogue and celebration and battle, which totals to a grand sum of zero storytelling.
Another problem with this movie is how it blows the scope wide open. In the original Matrix, you were given the sense that Morpheus' ship was the only hovercraft, and that Zion was some faraway place. In this movie, we are introduced to more hovercrafts, and gain the impression that Zion is an easily accessible place after all. It wouldn't be such a big deal, except that it damages certain assumptions you may have made after the first movie.
A few things that could have been explained better:
- Why is The Matrix still the battleground when Neo changed the rules?
- Why is it necessary for Neo to meet with the Oracle again?
- Why do they have to find the Keymaker?
- Who is the Architect and what purpose does he serve? What is his place in the story?
I think by now you get the idea. I'm not a big fan of this film.