I am a big fan of animation, so it is hard for me to try to single one out. I had to include shorts in the selection process because the prompt technically doesn’t exclude them.
The only followup material to The Matrix that I liked was in The Animatrix. The Second Renaissance wowed me when I first watched it, and I still think that it is well done even with the gaping plot holes. I tend to dig the work of Mahiro Maeda, the animation in Kill Bill is near the top of my list as well.