We also know, that http://elderscrolls.wikia.com/wiki/Dwemer were present in the late years of the Merethic era, before the http://elderscrolls.wikia.com/wiki/First_Era. "most notably in the Vvardenfell region"
Where am I going with this? Miraak's sword benifits from the Dwarven perk. Is it far fetched to wonder that perhaps he was Dwemer himself?