I don't mean to ruin your theories or rain on your parade, but Itachi didn't really know Naruto very well, except as the vessel for the Kyuubi. They really didn't interact much in the manga, unless they were fighting. I don't think Itachi would have thought Naruto was strong enough to be worthy of one of the treasures.
As for the tomoe marking both the Sage of Six Paths and Naruto, I think this may be the Sage's own kind of "signature" he left when he created the Kyuubi and all the other bijuu.
I have at least three very different theories on this subject myself:
1. Itachi left the Magatama jewel(s) in Sasuke, not Naruto. Remember, Itachi wants Sasuke to be able to kill Madara, and I doubt he thought that just putting his Amaterasu in Sasuke's eye would be enough. Itachi could have had many, many opportunities to do this, as he was with Sasuke much more than he was with Naruto, and especially in Sasuke's head, where he could have implanted the jewels. It could be that Itachi wanted to defeat Madara and control the Kyuubi. Susano'o is very powerful, but against the Kyuubi's power, it would likely lose. It's at least almost plausible that Itachi gave Sasuke the jewels or the way to the jewels just in case he came into contact with the Kyuubi's power.
2. The tomoe of the Sharingan themselves are the Magatama jewel(s). There are a total of six (three for each eye), and after you gain all three tomoe, the way is opened to gain Amaterasu, Tsukuyomi, and Susano'o. Susano'o is the way to find the Yata Mirror and the Sword of Totsuka. So, perhaps the jewel(s) are there, but are used as the tool to gain more useful treasures.
3. There are no Magatama jewels in the Naruto universe. The Susano'o itself is extremely powerful, and coupled with the Yata Mirror and the Sword of Totsuka, it's fair to say that it's unbeatable. There's currently no reason to increase its power even more, unless there's something that can rival the strength of Susano'o.