The machines need humans.
I was just thinking. If the Matrix is destroyed, the machines will still exist. The Matrix was created to house and controll the energy supply. Machines don't live in the Matrix. The free humans would now face the physical war their ancestors lost a long time ago. With much less resources now they don't stand a chance.
In fact the more I think about it the more I don't buy the whole human battery thing. The Sun is not the only energy source. Geothermal energy, nuclear energy, heck even fossil feuls are not dependant on the sun to produce. Why don't the machines use them? I think they need humans. They are interested in real life because it is the one thing they can never create. The Matrix somehow satisfies a curiosity. Incidentally how is Zion powered? Is there a Mini Matrix powering it? If the inhabitants of Zion dug a little deeper under the power generating room they might be in for a nasty surprise.