Shower thought of the day: I would like it if the real world machines are not even the threat in this movie. In fact, they did Neo and Trinity a solid by bringing them back to life, perhaps out of respect for him saving them from destruction. The villains would actually be both humans and programs who want to manipulate the powerful (but apparently clueless) Neo to their own nefarious plots, risking yet another war.
Basically I like more nuance from the machines, the kind we saw in the latter half of the trilogy. Rather than straight up "muhahaha!" evil, we get moments like "There are levels of survival we are prepared to accept", Rama telling Neo programs can fall in love, the babyface machine 'leader' acting petulant, and the reverent way they dragged Neo's body away (and choosing not to liquefy him or Trinity).
As much as I like good/bad dynamics in stories like Terminator/Alien, I also appreciate what the trilogy tried to do and give us something different. Rather than give us an enemy to hate (especially during the manic height of the Iraq war), it wanted to have us understand an adversary and give context for their side. Even Smith, the madman, had a compelling motivation throughout the trilogy.