Maybe shisui survived and a zetsu found his body and fused with him or healed him in a way similar to zetsu/obito.
Maybe Shisui then got the eye that was in Madara's eyesocket when he died. What if Shisui has been spying on and watching Obito/zetsu this whole time and keeping a small watch over the leaf and its enemies.
How this happened, what if after Shisui jumped off the cliff into Nakano River, Zetsu retrieved his body. Shisui did say he wanted to erase his existence. Itachi got his ninja way from Shisui and portrayed a bad guy to help the good guys secretly.
What if Shisui portrayed a dead guy, to help the living guys ? 
Shisui could have 1 eye just like Obito did , by taking the eye that was in Madara's corpse. Madara died with 1 sharingan in his eye socket, but he was revived without it. Either Obito took it or someone else did.