Manga factually speaking:
Rinnegan > EMS
Logically speaking:
Nagato can fly, giving him the ability to dodge Perfect Susano'o.
Nagato can also use Shinra Tensei to completely obliterate mountains at a time, so Perfect Susano'o is matched.
Nagato could possibly have a lower interval time/no interval time and that will be the end of Madara.
I don't see EMS Madara stepping up to the man who was called God.
Rinnegan > EMS
Logically speaking:
Nagato can fly, giving him the ability to dodge Perfect Susano'o.
Nagato can also use Shinra Tensei to completely obliterate mountains at a time, so Perfect Susano'o is matched.
Nagato could possibly have a lower interval time/no interval time and that will be the end of Madara.
I don't see EMS Madara stepping up to the man who was called God.