As cheesy as it sounds, afterwards I sort of felt like the bad cg (and copy pasting assets) was intentional. Maybe it was meant to contrast the eva specific parts with the rest of the regularly animated sequences with human characters. The scene that made me think this way was near the end the giant Rei head exploded into a bunch of 3d eva models (about 2:20), where afterwards they decided to animate the contrasting scene with humans without 3d, which was probably so much more work that I felt it must have been intentional for some reason.