Okay, first off... people tend to make a common mistake with Madara's eyes. They aren't really his eyes. The eyes that he had, that he gave to Nagato, that Obito currently has... actually belong to Izuna. They are Izuna's eyes.
So what really happened to Madara's real eyes? Were they just lost through time?
Further more... since Madara's eyes really belong to Izuna... couldn't Kabuto have also revived Izuna using the DNA from the eyes (Pain was already dead, and Obito only took one eye) and revived Izuna through the Edo Tensei?
Finally... In order to gain the EMS, you must first have the Mangekyo Sharingan (correct me I'm wrong), and obtain your siblings eyes (again... correct me if I am wrong).
Now... bear with me for a second on this one... considering that Madara and Izuna both had Mangekyo, couldn't they have just switched eyes and both obtained EMS? It is said that Izuna willingly gave Madara his eyes (Obito said this), while Itachi said that Madara took them by force. Yet, if both brothers had Mangekyo and were alive at the same time, couldn't they have switched eyes and both had EMS?
I was reading Izuna's page on Naruto wikia, and it said that he still lived after Madara had his eyes.
"Izuna later died honourably in battle, fighting to the death even in his blind state" - Naruto Wikia
Izuna died in battle, not because his eyes were taken. So that means that Madara had EMS while Izuna was still alive. So couldn't they have just switched eyes and both obtained EMS?