I think it went something like this, Houdini was used
for the little bug thing that gets planted into Neo, and the mirror scene.
Then Sentinels, Nebuchadnezzer, Fetus field, Docbot were animated in maya,
and all the bullettime stuff was Softimage. Heres a link to the vfxpro
article, http://vfxpro.com/.getarticle/.846504189 heres an excerpt form
it,
combined some procedural and blend-shape animation with a lot of keyframe animation. The procedural and blend-shape animation were useful for animation timing and rough blocking, but keyframe animation was always needed to add the nuances and character that bring these creatures to life.
HTH
E