Just looked like a substitution to me...maybe you guys are overthinking this.And I don't think Sasuke would necessarily have better genjutsu, I don't think he's shown tsukuyomi yet.
Genjutsu?
Something dawned on me whilst watching the latest ep of the anime... Madara said that when the 3rd died Itachi returned to the village to let them know he was alive and around so as to not touch sasuke. He also said that Itachi told danzou should he ever touch sasuke he would tell the world about what the village elders had done... I am beginning to think it's a failsafe like with the 4th and Naruto or the amateratsu and madara... I think it's Tsukiyomi that was implanted by itachi to protect sasuke against danzou.