It is interesting that, in recent chapters, Kabuto still makes a point to mention Shisui, Madara still coveted Shisui's eye, and Ao made such a point about Shisui's unique powers. You'd think there's gotta be something more to Shisui's role with Madara/Danzou/The Uchiha Massacre than simply "the powerful guy Itachi killed"...

Anyway, I don't have any real proof, just suspicion, but I think there's got to be a reason Shisui keeps coming up.