The eyes of the Sage of the Six Paths don't have tomoes on it. But when he was trying to control the Jyubi, we could six tomoes on its eyes overlapping some of the 6 ripples. I think the tomoes are actually part of the Jyubu's eye and has nothing to do with the Sage. Remember when nature chakra and kyubis chakra mixed, we can see Naruto's toad eyes overlapping the Kyubi's eyes. The same thing must have happened with the Jyubi's eyes while the Sage was attempting to control it with the rinnegan.
The Sage must have passed some of the Jyubi's sinister chakra, which is stored inside of him, to one of its offspring who could be the Older Brother. Somehow, someway... the Jyubi's evil chakra must have contaminated the Sage's DNA. Now, we can see that there are no tomoes on the Older brother eyes. Maybe at first, it was a recessive trait. As generation passed, It became more dominant and dominant. This sinister chakra might only be awaken through traumatic experience or through doing evil deeds. One doujutso clan must have accidentally awaken it and discovered the power that comes along with it. So they turned it into a practice to further increase their power. Thus, the Uchiha clan was formed.
This must also be the reason how come the Uchiha clan has an affinity with the tailed beast. And it is easier for them to control it.
In the end, it's not only a recurring battle between the older brother (Sasuke) and the younger brother Naruto but also a recurring battle between the Sage (Naruto) and the Jyubi (Madara).