There are some plot difference's....
1. - Naruto is dead. He can be revived by certain forbidden jutsu, but Sasuke killed him at the battle of the waterfall, giving him the Magnekyou Sharingan.
2. - Itachi is alive, in two halves, in the battle against sasuke, he was about to die, and used a forbidden jutsu to split him in two, one half is a 'good' itachi, who is currently an anbu at knoha, the other is an 'evil' itachi, who didn't survive the jutsu, this move gave sasuke the eternal Magnekyou Sharingan. The 'good' Itachi managed to revive him.
Summary - Naruto = Dead. Sasuke = Eternal Magnekyou Sharingan. Itachi = Two halves; 'Good' Itachi = Anbu. 'Evil' Itachi = Akatsuki.
Hope that's not to confusin. x3