Mark my words. It WILL be Shusui.
That Kotoamastukami that he cast on Danzo was meant to brainwash the old man into not doubting the validity of his upcoming death. Danzo got away with stealing one of his eyes, and when word came out that Itachi had killed him and the other eye was missing, he never once doubted that Shisui was indeed dead. Later during the massacre Itachi stole a pair of SG's from one of his clansmen, horribly disfiguring his face to conceal the act, and smuggled the stolen pair of SG's to Shusui as replacements for his own. Itachi then joined Akatsuki and we all know how his story played out from there. Unknown to the rest of the world, Shusui has been running around this whole time keeping tabs on everyone and acting as one final "fail safe" in case a situation just like were ever to incur.
Most easily plausible theory right now. At least better the Shikaku, lol.
Last edited by ask me anything; 02-18-2014 at 08:44 PM.