Here's my current theory on what the machines are and how the world came to be:
I don't think it was a terminator-style intentional elimination of the humans. I think humans created AI (although not necessarily human level) and that the AI just had the natural desire to survive and propagate because it was essentially a living thing. Somehow, the natural survival drive of the machines conflicted with humans, though again, not in a warfare sense - more just separate species competing. The machines simply out competed the humans. Most likely, there is also something they changed about the nature of the world (targeted EMPs?) so that technology that wasn't them simply doesn't work. Then they begin to evolve like wildlife. They did it very quickly, and a thousand years later we have robotic wildlife that is a part of the ecosystem and has probably replaced most large animals.
Humans weren't eliminated, but most died and all their infrastructure and electronic record keeping vanished/collapsed. Especially since they were more advanced than modern day, the loss was even more devastating and led to the collapse of large-scale civilization. Unable to use complex technology, humans returned to hunter-gatherer lifestyle. Even if I'm wrong with EMP theory, I don't think an explanation is necessary for why most humans live that way - culture does not have a direction and society does not automatically move towards more advanced technology.
Now, the humans use the mechanical processes of the machines (which seem like they process organic matter into... something. Food? Most likely) to survive. They incorporate aspects of the machines into their tools because it's high quality metal that can damage the machines. The machines are simply evolving and surviving. I suspect that they reproduce in a relatively natural, animalistic way - probably not sex and babies, but I bet they don't have factories set up anywhere. I don't think anyone is pulling the strings, I don't there's a hive mind or supreme AI, and I don't think they're all necessarily on the same side. They process organic matter as an energy source (think ethanol) and possibly as a remnant of the functions humans originally built them for. They aren't intelligent because intelligence isn't always advantageous - most organisms succeed without human-level intelligence.