Theres probably some fun ways this could be explored.
Like. the real world in the Matrix sucks. Theres lots of discussion on how Cypher was right. Not just the surface "comfortable lie", but in the our entire lives are lies. what we see is filter through eyes, which can be defective, and have limited scopes. ears the same. History even in the real world is written by the victors as they say. propaganda, etc as well.
what DOES steak taste like? What does ambrosia of the gods taste like?
Let the machines reclaim the Earth, while we chill out in the Matrix, seems a very sound option, even if humans and machines are at peace.
But, moreso. Machines can take over human bodies, as per the later movies. and/or the Matrix as a learning tool or vacation spot. Neo had kungfu training injected directly into him.
The matrix then would still have lots of use, even with awoken humans.
one fun idea might be autopiloting. Humans GIVING their bodies to machines to pilot, when they are doing some monotonous task for example. Letting the A.I. program take over, while planting a field of crops for example. the human mind, chilling out in the Matrix skydiving or some shit. and coming back to their body after the jobs done.
now, these scenarios have obvious vectors for how some hostile faction could do bad things. Trapping humans in the matrix again, taking control over their bodies in the real world, etc.