I've been pondering about it for a while: Madara or Tobi being right about the non-existence of perpetual peace. If the whole shinobi system finishes, nobody would train to become a ninja. If there are no hostilities and seek for power, why would anyone bother becoming strong? What's the use of Naruto becoming a Hokage?
So seen from this angle the end of the series is kind of self-evident.