Board Thread:Theories and Speculation/@comment-890307-20161205161301/@comment-25122992-20161218161333

There hasn't been mentioned any way to "merge" the two sets of eyes, the exchange of the eyes is the most logical and realistic scenario. And it was clearly stated that not every MS eyes can be used to unlock the EMS, these must be the eyes of a close relative, ideally a sibling. Madara surely wasn't a close relative of Obito, thus the latter's MS wasn't supposed to become an EMS in Madara's eye socket in the fisrt place. Also, there are the factors of it being a single eye (and the full power of a doujutsu can be unlocked only as pair of the same eyes) and Madara already achieving the doujutsu above an MS, i.e. the Rinnegan.

Well, what really matters is the fact the eyes are cured from the blindness, not how they are cured. Itachi impicilty said that Izuna's MS got an eternal light when its ownership was changed to Madara, thus becoming a more powerful doujutsu known as EMS, all thanks to this exchange. Moreover, I think that the interaction between the chakra of the original MS user preserved in the transplanted eyes and the chakra of the new owner results in the eyes themselves getting stronger than they were before, which includes the ocular powers getting a powerup and the elimination of the blindness drawback. Even if some merging process exists, it happents between the different chakra types within the transplanted eys, not literelly between two different sets of eyes.