Shins Body possessing Shisuis Chakra. Said so by Ao when he saw Danzo right Eye and Arm. One of them coming from Shin. Shins control over his Doujutsu. And Shisuis corpse which was never founded.
What do you Guys think about that?
And pls dont come with "..and he hated Sasuke for killing Itachi" When Shin is truly Shisui he knew about Itachis Mission and why he did that, and that he have to die for Sasukes Sake. But when he isnt Shisui he only knows the public version of his story and would think that he did that to get stronger.
The Gaiden was a mess, Shin half-assed character... just rushed. I feel that had the Gaiden been longer, Shin should have been Shisui. Also no explanation for Shisui chakra in Shin's arm. Orochimaru said Shin ain't a true Uchiha, how come his clones have Sharingan then?
Maybe they created copies of "shins" Mangekyou and transplanted them into the clones. This would explain (maybe) why Shins right Eye was black. This could of happened while they were experimenting on the Sharingan.