Madara and Izuna should have exchanged MS soon after awakening them. They would both have EMS and eventually the Rinnegan. I guess they didn't know any better. They were the first to ever awaken those eyes. It would be neat if that is what they did and devised a long drawn out plot to take over the world.
Another thought I had was was maybe Madara made the original Zetsu. If Izuna died shortly after having his eyes removed his body could well have been decayed beyond reviving. Maybe Madara used the Outer Path to bring Izuna's soul back and put it inside Zetsu. Maybe Tobi is the first Zetsu and is made up of Izuna and Hashirama's DNA.
Another thought I had was was maybe Madara made the original Zetsu. If Izuna died shortly after having his eyes removed his body could well have been decayed beyond reviving. Maybe Madara used the Outer Path to bring Izuna's soul back and put it inside Zetsu. Maybe Tobi is the first Zetsu and is made up of Izuna and Hashirama's DNA.