I think Anduin's presence is more about after the war. His working with both factions, his friendship with the Sunwalkers... His "I think the people of the Alliance AND the Horde are basically good" speech to Xuen... Says a lot about the future between the Alliance and the Horde - that they can STILL work together, and be friendly with each other when greater ambitions happen. When Anduin is King of Stormwind, and a less crazy leader (Baine? Vol'Jin?) is warchief of the Horde, they'll unite peacefully, stomp the rest of the old gods, finish off the Burning Legion, and meet the Titans (of course that part of the story can't happen as long as WoW exists, if only because it's necessary for gameplay.)
Questing also kinda reminds us that it's a new land, with new people, it's not "ours" and that there are still bigger fish to fry than the petty little war. Kun-Lai, Townlong and Dread Wastes can be seen as not only trying to protect this new land so that whatever side doesn't conquer it only to have it taken from beneath them, but also defending it so the Pandaren won't kick us out.
Honestly, I think the Sha are being built up as a Star Trek-style social commentary on why war is bad. The neutral factions are going to be there to drive the point home when the war explodes onto Pandaria, when things go from "dark clouds on the horizon" to full on "s---storm," and the players are going to be the ones who eventually work together to clean up the mess they made (and perhaps bring the war back to cold-war levels as it was in Vanilla and TBC.)
I think there's still plenty of war, or at least plenty of set-up. The Alliance and Horde bases being set up in Kun-Lai with help from Pandaren, the Monkeys and Fish-people chosing sides, the establishment of each factions' "capitol" in the Vale... The war is just being set up, it hasn't come to Pandaria in full force yet.
Edited by Auryanna on 10/6/2012 12:32 PM PDT