Aight here is my theory B aside from my spoiler. First off Omega a plan B? The machines dont and wouldnt need a plan B, they are machines they are perfect, there is no way you can beat a machine, the machines would perfect 1 Matrix so they wouldnt have to have a billion other Matrixs. Also Neo having super powers...blah he should have super powers if he is the One should'nt he?...Oh I forgot he is'nt.
Learning and adapting makes you weak, honestly who wants to learn? No one thats still kind of sad for our civiliztion though, but see the machines could boot up every piece of info ever discovered in like a day.
Actually in the Matrix the humans should'nt stand a chance because machines are better then we, I mean its kind of ironic that we have to depend on them.