I'd do something that might rustle huge amount of fanbases...
During Itachi Vs Sasuke, when Orochimaru appears... I'd make him take over Itachi's body instead of Sasuke's and taking Sasuke too because he'd provide him the spare set of Sharingan for the EMS...
Kabuto's purpose is done, he feels insecure and let Konoha know about all of it, and help them recover Sasuke but Sasuke doesn't want to tag along and goes rogue and later joins akatsuki, things move as in manga but knowing about Jiraiya's death, Orochimaru helps Konoha and Naruto against Pain's invasion... Gets Tobi's attention, tobi happens to be Madara... Orochimaru fights Madara or as it was said the shell of the former and defeats him, Sasuke backstabs Orochimaru takes over him again... Becomes final villain.
Working on the ending though...