I think the MVP's should be broken up between the sides of the war... the evil side and the good (shinobi alliance) side. But the war's not over so we can't really give an MVP just yet...
But so far my votes are between
Madara (evil) - Decimated the Kage, helped Obito when he was starting to get squashed, and even whiped the floor with Hokages 1, 2, and 4. Waited for Obito to get defeated and then siezed his opportunity to become a more complete Juubi Jin. Madara pretty much has the evil MVP on lock.
Kabuto (evil) - Brought Edo Tensei to the table for this war. Revived Madara when Obito wasn't gonna do that, so you could argue that Kabuto deserves MVP since he brought Madara back. However that's pretty cheap and I'm not gonna do that.
Kurama (good) - That's right, Kurama deserves MVP more so than Naruto does. Kurama was the source of the significant chakra that helped Naruto fight, Kurama also told gaara about plans to revive Naruto, and gave Naruto, Gai, and Kakashi intel on the Juubi. Also, it was Kurama's chakra that healed everyone, Naruto simply acted as a bridge to deliver the chakra.
Minato (good) - Minato made Kurama available in this war, saved the alliance from a Juubi TBB, saved the alliance again from multiple TBB inside a barrier by teleporting everyone out.