I Don't Think Shisui Is Dead
I've been looking into Shisui's bio lately, trying to figure out his relationship with Itachi, and this sudden thought crossed my mind.
What if Shisui is actually still alive?
For one, he's able to freely manipulate people's minds without them and he's a powerful genjutsu user, as stated by Itachi. So if you think about it, he could have easily faked and made other people, including Itachi, believe that he died.
Second, Kabuto was unable to locate his body to revive him from the dead; perhaps he couldn't bring him back because he was never dead to begin with? I don't think Shisui could have destroyed his corpse, leaving no traces behind, and, not to mention, Kishimoto never went into much detail telling about how he did it. (Itachi isn't much of a reliable source either; perhaps he's helping hide Shisui's existence, or maybe Shisui manipulated him with the Kotoamatsuki.)
And this is going on a stretch, but maybe Shisui is masquerading as Tobi? It isn't 100% confirmed that Tobi is Madara. Also, it is hinted that the real Madara is dead, seeing that he got revived by the Edo Tensei. (And Shisui wasn't.) Not to mention, if you look at Tobi and Shisui's hairstyle, it's rather similar. Besides, we haven't seen Tobi's actual face yet. The mask can hide so much~
I think (and hope) that Kishimoto's leading to the story of Shisui somewhere. It would be so interesting if Itachi tracked down Tobi (who's working with Kabuto, the user of the Edo Tensei) and find out that he's actually Shisui.
Questions That A Lot Of You Have Asked And That I'll Attempt To Verify
So a lot of you are asking me, or telling me for the matter, that there's no way Shisui could have survived after losing both of his eyes. I'm not saying that you're wrong; however, a person can still live with both eyes gone. While it'll be hard to function, it's still possible.
And my theory on his eyes: he could have held onto replacement eyes before losing them to Danzo and Itachi. Transplant - Kakashi had Obito's eyes transplanted and that's how he got the Sharingan, therefore, it's a definite possibility. Shisui could have easily done it, considering that he's a genius.
And it seems like a lot of you are skipping my "manipulation and genjutsu" proclamation. His ability to manipulate peoples' minds without them noticing is not stated without reason. If he was so good at manipulation, then Itachi and the police force were no exception. He could have played them easily. The body that the police force found, if they found it (I don't think they did, but one of you said it - wasn't his body in-discoverable or was it visibly destroyed?) could have been a pseudo-body. Genjutsu could have made it look as though his body was destroyed when he was actually just setting it up for an escape.
Also, keep in mind that Shisui excelled in the "body-flicker" technique. Tobi shares the same technique, and we've all seen it: a blade can pass through the user's body and not kill him. Faking death - basic Ninja tactic.
Again, this is just a theory. I'm sorry if I'm making Shisui sound like a bad guy, but if it makes you feel any better, then maybe he's doing all these bad things for a good cause (like Itachi~). I guess all we can do is wait for Kishimoto to release the facts!