The one time we see Shisui's Susanoo, it has a glowing red tomoe in its chest.
Given that the other two Imperial Treasures of Japan are in Naruto (Itachi's Susanoo had the Yata Mirror and the Totsuka Sword [which has some parallels/connections with the story of how the Kusanagi sword came to be in Shinto mythology], and Orochimaru had the Kusanagi sword), does anyone think perhaps this was supposed to be the Yasakani jewel?
I'm guessing Kishimoto had plans for Shisui to be more involved in the overall Naruto story and get more screentime and "pagetime", which would eventually lead to it being stated that the red tomoe in its chest was in fact the Yasakani jewel, and perhaps something about a mission Itachi and Shisui went on to recover the Imperial Treasures and they ended up giving them to their Susanoos or something. Thoughts?
About Kishimoto having plans for Shisui, I doubt it. Perhaps a flashback, but for him to get more involved in the overall story, no. Unless the mangaka hadn't decided from the start who Tobi would be, and Kakashi Gaiden was just a way to buy time and make readers think the mysterious individual was Obito.
No, the Yasaka Magatama is not it. The individual projectiles are shaped like the Yasakani, but the Yasakani's shape isn't exactly unique or uncommon in Naruto (tomoe are everywhere in this series), and the Yasaka Magatama attack is produced from the Susanoo's body/miasma, whereas the tomoe-shaped thing in Shisui's Susanoo doesn't seem to be (as it is a totally different color than that of his Susanoo and he never has his Susanoo use it as a weapon or separates it from his Susanoo's body). Also, the Yata Mirror, Kusanagi, and Totsuka sword are also all specifically talked about in the series as super-duper-special-and-unique, one-of-a-kind objects and weapons, whereas the Yasaka Magatama is described as a technique derived from the the Susanoo, an "any sufficiently developed Susanoo (or at least many sufficiently-developed Susanoo) can do this" kind of thing.
Saying the Yasaka Magatama is the Yasakani jewel is nonsensical and basically equivalent to saying that it simply doesn't exist in Naruto (and perhaps was never planned to), which is the answer I'd find more logical.