How was scientist Jor-El kicking so much ass and killing the legions of bad guys? He even managed to fight off Zod, who should realistically be the deadliest man on the planet if he was bred for war and to be a General and the Defender of Krypton. It was poor/lazy writing to me.
Well even without being bred for it, it's possible all Kryptonians are just naturally very strong and good at fighting.
Or maybe, given the fact he already decided to break taboo and have a natural child, Jor-El's "programming" was a bit off and different from the others.
Which sort of begs the question.... If Kryptonians had been breed to be birthed by the robots from The Matrix why were they given the ability to breed in the first place? What does Jor-El need a penis for and what does Lara need a vagina for? Hell, what are men and women needed for at that point? If you can just make whatever/whomever you want and don't need people to actually get-down to make people; gender and biological procreation is useless.
They may not need
any sexual organs, but I imagine when they came up with this technology, that was something they decided they still VERY much wanted to keep.