For one, he hasn't needed to use his EMS yet. And second, he did mention that he still carries the injuries he suffered facing the 1st, so it's possible that he may not be able to use the EMS at this point in time due to something the 1st did to him.
As for Kakashi's MS jutsu and Madara's eye technique, other than them both being Space/Time techniques, there's no deeper link between the two.





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