The Matrix: The Machines Got It Wrong On Energy
Then Morpheus told Neo that the machines combined a sort of fusion power to supplement using humans as a power supply. Well if they perfected any type of fusion they surely would not have needed to develop, maintain and manage a human-powered 'battery' system. Utilizing the heat from humans would be an incredibly inefficient use of time and well, food to feed the humans. Maybe it is just a good science fiction image but makes no sense in science. Fusion power is the holy grail of energy systems and works much like the Sun, but I doubt that even the machines could have perfected its use in the 21st Century, when The Matrix takes place.
The Wachowski Brothers were being politically correct. Actually, because the machines would not have to worry about negative health effects, they could have used coal to produce electricity. America alone is the Saudi Arabia of coal. The machines could have used nuclear power plants, including converting U-238 to plutonium (U-239), which would provide an almost limitless supply of nuclear fuel, particularly if the machines reprocessed and recycled it. The machines would have also utilized natural gas and oil. All of these would be much more efficient and effective than human conversion. Even ocean power and wind would be better. Come on Wachowskis. Clean this up in the next trilogy (no pun intended). The interesting thing would be that now that the humans are being freed, the machines and humans would have to figure out which energy sources to use now in order to keep the Earth comfortable for human habitation.