All of this could have been avoided if the 3rd had sacrificed himselfin the first episode. Allow me to explain:
The 3rd sacrifices himself to seal Kyuubi. The 4th reigns as Hokage. The Uchihas are afraid to mess with the 4th, so they put their plot on hold. When Orochimaru attacks, the 4th is easily able to overpower and kill him. Sasuke, no longer corrupted by Orochimaru and Danzou, studies under the 4th with Naruto. Itachi and Sasuke trade eyes, both permanently gaining the EMS. Akatsuki's forces are crippled by the lack of Itachi, Orochimaru, Sasuke and the Sasukettes. Itachi, the 4th, Naruto, Jiraiya and Sasuke are easily able to overwhelm them. When Itachi takes over the Uchiha clan, he is horrified by their plot and permanently terminates it. Naruto follows in his father's footsteps and becomes Hokage. Everyone lives happily ever after.
Damn, Konoha, you guys should just ask me what to do next time! I could have your village a ton of problems!