The gist of it being that The Matrix is yet one more example of Hollywood bad guys being stupid.
Exhibit A, why do the machine grown people still apparently have sex organs. I seriously doubt Neo would have been getting it on with Trinity if he looked like a ken doll down there. I'll put it terms that even those dumbass machines would understand;
The reason why the machines shouldn't want their machine grown fuel to have sexual organs is simple; once Neo figures out what to do it won't be long until there are five or six little neos ready to wreck shit all up and down the machine capital of 01. This argument holds true even without The One; I can't speak for everyone, but I know for myself that if I was chilling in Zion and there were only a few thousand people left I would definitely be doing my patriotic duty and knocking up every chick in sight. I know that Zion is a small town, but there would be at least ten other men like me. Before long us, eleven horny, bastards would have grown our own army. So the machines are stupid for not deleting the sex organs of their batteries, but there is something they didn't do that is even more stupid.
limManhood → 0+ Life = PENIS
This one is so obvious that I should kill myself and everyone else who didn't notice this the first time they saw The Matrix. Why do the machine grown people have arms and legs? This can only lead to trouble, but apparently after like eight tries those retarded machines still didn't figure it out. Since we never saw Neo fly in the real world we can only assume that he can't fly in the real world. The One wouldn't be able to get much done in a world mostly populated by human inchworms, especially when he himself was also a human inchworm. One might make the erroneous argument that the machines left the arms and legs on the people because it was a more efficient producer of energy. Even if you ignore the fact the machines had no problem producing vast quantities of people; one can't ignore the fact that roughly ninety five percent of a humans body heat is concentrated in their head and their torso. So why risk the possibility of being overthrown by your own fuel source when you can just genetically engineer them without the means to ruin your shit; and growing another five extra physically handicapped humans per one hundred normal ones wouldn't be that big of a problem. Especially with the extra security you would gain from doing things that way.
In conclusion the machines are stupid and The Matrices, while decent movies, are also stupid as are most movies. In fact people should start reading books instead of going to movies their plots are still just as full of holes, but at least you can sell a book to a used book store and recoup some of your losses; I've never met anyone dumb enough to buy a used movie ticket. Maybe I should try to find those machines.