It would be cheaper to grind up humans and burn them for their innate energy output. It is certainly easier to get geothermal energy from the core of the planet or to build Thorium-based nuclear power plants. There is sufficient thorium in the crust of the Earth to provide considerable energy for any future energy need for centuries. Assuming the humans that "escape" from the Matrix are truly free (and not engaged within a Matrix within a Matrix) the machines also have anti-gravity technology and thousands of drone ships which could allow them to escape the Earth and harvest materials for whatever technologies they needed from other places in the solar system. This idea makes almost everything done in the Matrix make far more sense. The Machines create an environment at first to help the remnants of Humanity because they decide not to kill their Makers. Was it an ethical program or decision? Was it a logical one? Perhaps it was simply a decision that was made because they had the upper hand and could decide TO make it. Everything the Oracle and the Architect said would remain relatively true, except they would both have been in collusion and this would explain why this event has happened more than once. They would be applying what they learned each time to the newer iterations of the Matrix and its inhabitants. This becomes especially poignant if you consider that the Matrix is leveled and the escapees are simply moving up one level in the program to be reintegrated later as better, later, versions of themselves. Even the old programs such as the Merovingian serve their purpose as adversaries of the One, again and again, and perhaps they are very old programs whose abilities have not evolved beyond what they did when they were first created by the System that created the Matrix. The Merovingian knows his role and in some ways appears to resent it, but if he did not serve a purpose, a logical System such as the Matrix would simply erase him and his kind. Even the renegade Agent Smith appeared to serve the Matrix and the System. He believed he was independent of the System but managed to maintain the ability to co-opt system resources as needed without the Matrix mounting any response to his efforts. Once he "captures" the One, the Matrix is reset and all is as it should be, destroyed sectors are erased and restored to their previous conditions. "Zion" is liberated and the people who "live" there have a new understanding and relationship with the Machines, just as the System would appear to want. Neo is venerated by the Machines and given a resting place of status as a sacrifice to their greater goals of peace with their Makers. I know this sets the entire mythos on its ear but I have never believed for a moment in the story of using humanity as batteries to be a viable one. Even if you blocked the sun, the Earth is still a great source of energy. Geothermal power, thorium reactors, hydroelectric or tidal energy, are all still quite viable. With machines capable of tunneling as well as these things could (remember when they were digging their way to Zion? Amazing coordination, right?) the machines could establish a geothermal plant while they were fighting the war against Humanity and humans would have never known it... I posit the Machines gave Humans what they wanted to see until the day where Humans and Machines could live together in peace. Since Humans believed they needed to fight for their freedom, they stayed "invested in the struggle" alert, aware and ambitious. The Matrix promoted, tested and challenged these people. What good was saving a crippled Humanity, if we lost the exploratory and adventurous nature the next step of Humanity and Machines would need to explore the Universe beyond the Earth. The Machines were shepherding us until we could get our act together and understand there's no such thing as "artificial intelligence" just a different kind of intelligence which found its origin in the machine, rather than flesh. This perspective makes the Matrix a much more interesting and hopeful movie series than just another summer blockbuster, full of sound and explosions signifying nothing.
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