alt Hacker NewsThe Bene Gesserit tried to solve alignment through their breeding schedule, but Lady Jessica threw a wrench into it by bearing a son (Paul) out of love for Duke Leto. Paul wasn't aligned with the Bene Gesserit, and hilarity ensued.
So I agree, I don't see why thinking machines are a worse alignment problem than enhanced humans. See also the Wrath of Khan.
I try not to think too deeply about it, or I won't enjoy the story. How could a society have gravity suspensors, "shields", and lasguns, but no advanced computing capability somewhere? And why use swords/knives for fighting, when projectile weapons are so much more deadly? I still love the books, but I have friends who can't enjoy the Dune world due to its many contradictions.
Edit: I realize that "shields" supposedly made ordinary projectile weapons ineffective - but they had advanced drone technology (e.g. the assassin drone used against Paul, which was also stupid)
They had advanced computing, a whole region was full of it: IX.
The rest of the empire was too feudal and too religious to dabble into advanced technology. And the other players (the BG, the Tleilalxu, the Guild) were against it as well.
What good are drones, except as weapons of assassination? Can't use them in an conventional war, there are shields. And they're very expensive, remember, the Great Houses don't have advanced manufacturing capabilities (that's IX). And, finally, there are no great wars in the empire, most houses keep to their planetary fief; the Baron's attack on the Atreides' forces on Dune was an exception. It was also mindbogglingly expensive, 80 years of spice profit.