There is also a question of if after operation dark storm, was there any other power source suitable to be able to power all of the machines? Even if they did not have a law against genocide (which considering the resets that happen in the matrix killing all but 15? 16? whatever the number is not sure that law exists), like Operation Dark Storm was a last ditch effort, was this also a last ditch effort on the machines side.

But at the same time the theory that maybe they are against genocide in some form is backed up by Smith talking about how the original matrix was going to be a utopia. That doesn't seem like the kind of thing you would do to the people you are fighting (and just tried to wipe you out completely), if it wasn't for some ethical guidelines.

Fuel would be a limited resource. I know that a lot of people point out that on a biological sense it does not make sense, but we also see Neo being pretty frail when he wakes up. Does that biological problem still stand up when your body is frail and it is basically just your brain and basic processes. Throw in that your not eating real food, likely optimized for as little energy lost to process that food.

Something that I don't think any of the media touched on, but would it be crazy to think that the machines could have made genetic modifications to support this.