Nagato: The perfect inbred spawn.
With all the talk recently about Madara "giving Nagato his eyes" (which some people took literally) it just sparked my attention to Nagato himself so I came with this completely far-fetched, or is it o_O?, idea about how Nagato could've been lucky enough to be so something of a freak of nature so perfect to resemble the almighty ninja God:
As Madara said Nagato's signature Red hair was a testament to his Uzumaki Clan ancestry who were in turn distant relatives of the Senju. Since the Senju were the direct decendents of the sage's youngest son the Uzamaki's lineage branches off from the Sage's yongest son as well (which could be why they were known for having resilent bodies and longevity). We know Nagato has Uzumaki genes in him but what if his Rinnegan mutation was due to having combined Uzamaki and Uchiha genes? It could seem a likely reason since having both genes from the Sage's 2 sons could be the extremely likely catalyst to promote a great mutation such as the Rinnegan in the first place! How could it have happened? Seeing as how ninja back in those days were all about clan warfare and pledged the greatest alliagnce soley to their clan it would be rare for people from different clans to procreate with one another (imbreeding: yea, having sex with someone else from a different family: are you nuts?). Since the external beef with the Uchiha and Senju came to an end and the village system was born and the newly formed Konohagakure formed an official alliance with the Uzushiogakure then those 3 clans (Uzumaki, Senju and Uchiha) would've been in better contact with 1 another. Some stud reject Uchiha meets a sexy red head Uzumaki and they fall head over heals for each other but even though shit's ok with the clans now there was still a lot of animosity amongst the clans so Nagato's mom knew she couldn't show up to her parents house with that Black haired emo looking Uchiha boy that never looks like he's up to no good. So to escape this love halting prejudice they decide to leave their respected villages and move far away where they could live in peace. There they had a son who, being the result of their converging genes, mutates to form a being most resembling the Ninja sage himself.
If not that then Madara could've raped/used his slip between what ever place or dimension ability to slip between Nagato's mom's legs and spermed her knowing that combining their 2 history filled gene pools would have said effect on the child which he would then kill in.. say 20+ years so he can steal their eyes for his plan now :). Having the genes from both sons seems like a more likely reason for Nagato being the way he was rather than it just being a freak occurance in my book.