I think it marks the moment where Hollywood finally went, "average CGI is just as good as exquisite in camera and practical fx".
The big thing about the first Matrix being the wonderful wire work and bullet time. To sell that out with a Gary's mod version of Agent Smith was a real mis-step.
But I'm sticking with the sound effect and the reason being that they knew the CGI looked comical, so they leant into it with the bowling alley foley.
Rather than going, 'this doesn't work' they decided to make it a feature.