In the Matrix 3 Smith apparently overwrote his program onto every human and program in the Matrix.
If the humans continued to supply energy to the machines in this state, why wouldn't the machines have done something like this since the beginning (but keeping it under their control)?
I understand that the machines needed a Matrix to foster biological and neurological activity, but it seems like the same thing can and was achieved with the administratively assigned personality of Agent Smith overwriting the more problematic independent minds of humans in the Matrix.
Wouldn't that have been far less problematic for them, if they could get the electricity without having to deal with all of the potential escapees, the "balancing of the equation", the building and rebuilding of the Matrix, etc, etc?