Well, evolution occurs only when there is a need for it. It's basically gaining traits essential to survival. You could say that So6p's descendants didn't need the Rinnegan to survive in the world, since the super being called Jyubi was no longer there. On the other hand, it was thanks to So6p's Rinnegan that not only he survived, but the whole humanity up to this point could exist without fearing it's most supreme predator to this (Naruto) day, which is their source of existence anyway (ah those circles

). It's like with the autonomous system loosing it's capabilities if you live too long in a sterile environment, without germs and the like (this might be a great problem in a far away future).
This might explain why none of the So6p's descendants have been born with a Rinnegan spontaneously, unless we assume that not even once, have the bloodline been reunited, then they simply didn't have the right genes to obtain it.
Still, evolution is a very slow process, it doesn't normally occur at such radical speeds, which suggests that there was already a good groundwork of genes from which a Rinnegan could have been born, or a mutation have appeared, which turned out to be a great thing (rarely happens). There even are people who considers evolution as just a simple set of beneficial mutations. It is possible that an interaction which Jyubi might have caused the mutation (like eating it flesh and the like).
There is a certain type of energy (in narutoverse) that creates great changes to the human body, called Natural Energy. We have already seen it's effects varying from turning to stone, frog, reshaping your eye pupils to allowing you to freely morph your body the way you like.
BTW.: NEO GEO EVA is certainly a great series, which they are currently rebooting in the form of movies. I have to say that they are great, but a little less twisted I guess

, for now that is

.
Bookmarks