Why is it important to the Bene Gesserit to use the blood of Noblemen in their Kwisatz Haderach breeding program? Are there no other (possibly better) candidates that they could obtain genetic material from? What makes the Noblemen's blood so special?
Its not as much matter of genes but matter of control:
- Nobles are better protected: Its much more likely that your average Commoner would get killed or raped therefore destroying the line. Same goes to the children.
- Nobles (at least women) don't tend to have that many illegitimate children, because they have obligation to continue their lineage and produce heirs - hence if you marry Jane Highborn to John Aristocrat a you can be (almost) sure that he will be the father (not your friendly, neighbourhood postman) - it doesn't mean that they won't have lovers or bastards, just that there should be at least one TRUE heir.
- It would be easier for Bene Gesserit to orchestrate the desired marriage for a noble house rather than simple commoners - the former marry for political reasons, not for love.
- Matter of prestige - it DOES sounds better saying that your Ultimate Being is a child of noble house, rather than born from milkmaid, conceived in suspicious circumstances involving stable boy and too much beer. It would give such person much, much stronger political standing - after all BG can't simply point a finger at someone and say "Hey, that is the guy we've been planning to create for centuries, listen to him!"
The Bene Gesserit basically believe that the cream rises to the top, so that's where they focus their genetic efforts. They pick noblemen and other leadership types because they believe that for these people to distinguish themselves by rising to the top, that implies superior genetic potential.
In Heretics of Dune, Odrade has an encounter with Albertus, the senior of Dar-es-Balat, which demonstrates Bene Gesserit thinking on their genetic choices:
Albertus cleared his throat and took a trembling breath.
Weak bones! Weak flesh!
While the thought amused Odrade, it did not reduce her wariness. Reverend Mothers always noted that sort of thing. You looked for the marks of the breeding. Such selectivity as existed in the ancestry of Albertus carried flaws, elementals that the Sisterhood would try to correct in his descendants if it ever appeared worthwhile to breed him. This would be considered, of course. Albertus had risen to a position of power, doing it quietly but definitely, and it must be determined whether that implied valuable genetic material.
That's why they select noblemen and the like. They want the very best of humanity, and they believe that's where you find them.