Um, let's start at madara. He is/was Indra's reincarnation, so he has indras chakra. And how did he get ashura's chakra? By implanting senju cells. That combined gave him the rinnegan.
If you put it in the scenario that Kakashi would've been hit by the rock instead of Obito, Kakashi wouldn't have the sharigan which is a nerf to his skills really. And without Obito Akatsuki wouldn't be the same like it is now.