Hmm well I thought about it but it still could be Shisui, the ears, nose, mouth, the line below the mouth fit quite good. The more damage eye (left) is the one Danzo plucked out, while the normal looking one is the one he gave Itachi.
And it was never explicitly stated that he is the threat Kaguya knew about, who says that not the Mini-Jubi is the real conspirator or they all are just played by the "higher power". The Sharingan comes from the Jubi so why would the thing/person Kaguya feared have something that comes from the being she enslaved?
Also if there is something out there which frightened Kaguya in her prime so that she created a Zetsu army, you really think it would be some sharingan abomination with a weak clone army? They are probably just the Radditz of this story arc ;-).