Madara, for me. Everything that's going on in this storyline began with Madara (the relevant parts anyways).
- Project Tsuki no mi was Madara's initial idea, which was the reason for the 4th Shinbobi war.
- It was Madara who deceived Obito into gathering the beasts and one day reviving him in order to act upon the plan (this led to the formation of the Akatsuki and so forth).
Basically the entire story line is built upon something Madara had planned. With him being the current Juubi Jinchuriki, and everyone else being dead, I think it ultimately comes down to Sasuke and Naruto teaming up to defeat Madara, once and for all. All these legends like Kaguya, Hagoromo and the legendary brothers, is merely a plot device to not only supplement reasoning behind what Madara is doing, but to do add growth to the main characters (Naruto being reincarnation of Ashura etc..). I just cannot see anything else happening.
Lol at Orochimaru being the final villain.