Oh my goodness I've just learned a thing about The Matrix that causes it to make a lot more sense: In the original script the humans were used as neural network compute clusters by the Machines and as a crucial component of The Matrix itself.

Which is why humans who were aware of the simulation could control aspects of The Matrix - their minds were part of its foundation.

Unfortunately the test audiences had trouble understanding this concept so the studio changed the human role to "batteries".

Hyperion novel spoilers 

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