1. Madara goes into his dimension and talks with sasuke, telling him a few secrets he didn't mention to the kages.
2. While unlocking SG, MS, and rinnegan can allow you to read more and more of the uchiha stone tablet, the EMS can see a final hidden message.
3. We find out that madara didn't steal his brothers eyes like we think. Instead they both chose to switched. The younger brother didn't get EMS, instead unlocking rinnegan. After seeing the rinnegan allowed his brother to learn any elemental attack, he killed him and took his left eye for himself. He keeps it covered so no one will know.
4. Madara thinks sasuke's 6-point star design is just his MS. We find out it's really something way different. I've been thinking about this for a while now. When Itachi gave sasuke his MS tech, he did a lot more than just that. I think he actually altered his DNA to give him his abilities. These abilities lay dormant until triggered by certain events.We see that when sasuke used Amaterasu on madara his eye formed a replica of itachi's MS. That's 1 example. Itachi wanted madara to think Amaterasu was his plan to kill him, but in reality he knew it wouldn't work and wanted madara to recruit sasuke. He already knew all of madara's secrets (^referring to idea #3). Sasuke's activation of his MS, was a 2nd trigger. What happen was itachi's jutsu tricked sasuke's body into thinking the eye transfer had taken place. It was supposed to result in the EMS. If that's the case then we would see itachi's pattern over whatever sasuke's looked like, which we don't. That's because sasuke had the dormant rinnegan ability in his DNA, which also activated. It then integrated with sasuke's EMS forming a whole new eye tech.
Here's a scientific way to look at it. Human DNA is made of 46 chromosomes. Kekkei Genkai are mutated genes found in these chromosomes. Lets assume all the uchiha clan has the SG/MS ability, but most people will either have the EMS or rinnegan trait which is made from 2 different genes. Madara was born with the EMS trait. Izuna had the Rinnegan trait. So when madara and izuna switched they each unlocked different abilities. Madara just stole his brothers eye afterwards giving him one of each. When sasuke unlocked his MS, itachi's justsu activated his dormant DNA attempting to artificially create the EMS or rinnegan (whichever sasuke had), However an error occurred during the process, causing the EMS abilities to be inserted into the rinnegan chromosome, resulting in a completely new mutation with unforeseen powers.