I always looked at it as the man against machine gig ( great film trilogy btw definitely in my top 10 )
man creates machine,
machine gets smart,
man gets annihilated by machine,
machine takes over,
man fights back.
Not to sure if we weren't the best power source they could have found, though with a war on the magnitude they waged i wouldn't have thought that they were thinking much about animals more thinking about how to win it and take over. Then see what was left and worry about how to incorporate and extract the power, also i would imagine that they artificially produced humans to feed there ever increasing power need so could be that they found it easier to reproduce us than animals
There was a scene in the film were they were discussing tastes and food. the question posed was how did the machines know what chicken tasted like (amongst other things ) the answer was they didn't that’s why everything tastes like chicken

In life you make mistakes, but that's life. As long as you learn by the mistakes you make, don't be afraid to make them.