OT: Sakura meeting the Sage and Kaguya and obtaining both their powers, kills madara, gets both Naruto and Sasuke pregnant with her new powers, and then starts a dictatorship. She eventually dies with her neck broken as a result of slipping on an orange peel.
This comes from an incident in an RPG I played long ago on the Play Station.
Madara's battle goes from epic with Guy to being possessed by Kaguya and is KO'ed in a combined hit from Naruto and Sasuke because she wasn't strong enough to be fully revived.
Kaguya turns out to be an alien. Two beings from her home planet come to the NV to gain the Shinju's power in order to obtain immortality to be used to overthrow a galactic overlord named Freezara.
Naruto doesn't become Hokage or die. If he's not Hokage or dead then that will be the lamest thing ever, no one wants to see him traveling around the world preaching. Also the Ninja system not changing would be anit-climatic too since it was mentioned so many times