The best evidence for this is that suddenly the entire series starts making more sense. Why can't the machines just take off into space and leave humanity behind? Because they're still running on human meat. It makes sense that the humans shouldn't exactly have control over the simulation, but why do they have
any, like Neo? Because the simulation still has huge chunks running in human heads and that part can be influenced strangely, even though I think it's equally clear a great deal of the simulation is running on conventional computers too. (And yes, the Architect may goose that along, but he isn't creating it.) Why can Neo still influence the Matrix even when outside it? Because he still has some kind of subconscious connection to it, with wireless presumably provided by the gear in his body (+ whatever the Architect did). Why are the non-main characters such cardboard cutouts? They're literally running on only a fraction of their own brain; the exiles are the ones that for whatever reason, grew into their own brain more than the average person.
And I don't just mean "fanon" sense, though, yes, there's an element of that, but more actual sense.
It's still kinda a mess, even from this point of view, but it's pretty good for a Hollywood effort.