A thought occured to me earlier that, although it may not be the "final" secret, could be another one and would make sense of a few things. Hopefully nothing similar to this has come up before.

I believe MS has the ability to cancel other MS out. Madara stopped Amaterasu just as Sasuke did, so I don't really think it's something original to Sasuke, unless I'm just remembering incorrectly.
Spoiler!
Spoiler!
It was never shown how Madara really extinguished the flames, but it's possible he did it the same way Sasuke did. That's the first instance of it. The second that comes to mind is two Mangekyou merging. It "cancels out" the blindness, which is a side effect. If you think about it, why would a second MS have any resistance to going blind. I mean, it was before they were inserted in Madara's eye sockets. There really isn't a good basis to this theory and it's mostly assumption, but it seems to make sense in my eyes at least. I'm sure there were other pages where things could be explained by MS cancellation and I'm just forgetting, thoughts?

(I wonder how long it will take before this theory is disproven, lol)