I think they were too cryptic and the Wachowskis were consumed by the grandiosity of their own mythos, but they were still impressive for what they attempted to do: build a sci-fi epic.
This is why the Animatrix is great. It's divided into 9 episodes across various points in the timeline. Each episode was created by a different group, so you get 9 perspectives on the overall story.
having re-watched the original recently, one of the most striking things was how successfully they managed to create a setting that excuses practically every single convention of bad screenwriting and still works as a film.