I think personally the main difference is that the matrix novels were aggressively futurephilic right from that famous opening line.

The more recent novels are more tempered by demonstrating the present is a strange and wonderful place that is accessible in our own lives. That requires a non-aggressive feel.

I like both. The futurism and technophilia and edginess is more inspiring in work. I feel more bad ass. The modern day is wonderful novels remind me of the joy of living now and that I can actually live the dream I want.