I think the breeder I obtained my Shibas from is a pretty good example of a great, and very judicious breeder.
She obtained a *beautiful* black and tan Japanese import bitch. The markings were clear, and nearly perfect (hard to find these days), the coat of correct texture, and pigment (a dusky brown-black, NOT blue-black), and the bitch had a stunning headpiece and movement to die for. All the appropriate tests were done before any sort of breeding was to take place, and you can imagine her shock and surprise, that this lovely girl had a mild case of luxating patellas. Mild, but definitely present.
This dog, imported from Japan to the tune of $35,000 USD, was promptly spayed and placed in a pet home, for a nominal fee of $850 (the asking price for a pet puppy).
This girl *seemed* to have it all. She excelled in nearly every aspect of the breed. But sometimes all it takes is that one *little* fault. What may seem like a small deal (one luxating patella, a bit of an overbite), could in fact devestate an entire breeding program. No matter how exceptional the animal, if a fault is present that will affect it's life adversely, one that may easily get worse when passed on to puppies, the responsible thing is to cut your losses, enjoy the dog for it's individuality, and spay or neuter it.
Once you decide to breed that dog you are *stuck* with those genes in your program. There is no way to weed them out. (If you wish to continue using those lines). It is an irreversible process. By forgoing to breed the Shiba bitch with luxating patellas, my breeder suffered a bitter disappointment. But she saved herself *far* more heartache- the possibility of having a breeding program riddled with a pretty major flaw, one that would adversely affect future animal's lives.