Southern climes and a world reshaped by the unmaker
Frankly, one thing that could easily be worked into Mists of Pandaria is a South Seas patch that explains the new shape of the world following the Cataclysm. Not only is there now a new set of islands off the coast of Stormwind (islands that are just the mountain peaks rising from the underwater shelves of Vashj'ir) but we've seen no sign of Kul Tiras and we're told that some sort of disaster has befallen Zandalar Isle. You could easily add an entire zone or even several zones of undiscovered/unexplored islands to the north of Pandaria, lands that were pushed there, ripped from the ocean floor, or even created by volcanic eruptions or more exotic means. I can imagine an island torn from Deepholm when Deathwing punched through, with a chunk of the original World Pillar emitting strange cosmic forces warping both the original elemental inhabitants and any native Azerothian creatures caught in its influence.
One can easily imagine desperate Zandalari refugees turning to the Darkspears for aid, giving the Horde a base of operations in the area, while the people of Kul Tiras would open their ports to the Alliance in return for aid against all the new and strange things in these southern oceans, so far from their original home off the coast of the Eastern Kingdoms. I'm not saying this will happen, of course, just that it could. For that matter, it could just as easily be an expansion of its own, although I don't know if an entire expansion of island-hopping would be enough.
Still, a South Seas patch or expansion could at least up the stakes on the Horde/Alliance conflict as well as bring back Tandred Proudmoore, son of deceased Admiral Daelin Proudmoore and brother to current Kirin Tor leader Jaina Proudmoore. Tandred's never actually shown up before, and frankly it's long past the time he should have.
Turalyon and Alleria?
Completely unrelated to Mists, however, is the subject of Alleria and Turalyon ... except of course for the fact that it was in Mists that the loading screens started mentioning the two. This drives me crazy. Are they somewhere in Pandaria? Why would they be? If they are, what are they doing? Or perhaps it's not that they're in Pandaria, but that they're back on Azeroth or will be soon that's the important issue. Azeroth itself has changed greatly from the last time they walked on the world -- Silvermoon is now in the hands of the blood elves following the Scourge invasion, and the king that Alleria served is now dead. Her sisters stand on opposite sides of the factional divide, one living, one trapped in undeath, and for Alleria family was always paramount. It was the deaths of many of her family at the hands of Doomhammer's Horde and Zul'jin's Amani trolls that set her on the course of her life, that caused her to ally with Turalyon's forces in the first place. Meanwhile, for Turalyon he returns to a world where the majority of human kingdoms are gone, ruled by walking corpses or torn apart by discord. Only Stormwind remains, and of all the paladins of his generation, a paltry few remain.
The return of Turalyon and Alleria could create shockwaves that would amplify the war we currently have to one fought like the First and Second War, one fought with massive direct confrontations on the home territory of its combatants. Would Turalyon accept the Forsaken's right to hold Lordaeron, Gilneas, and Alterac? Would Alleria accept her sister as a walking corpse, her nation as allied to the same orcs that murdered her family? It's not hard to imagine High General Turalyon rallying hosts to his banner, or Alleria Windrunner bringing the scattered high elves from Outland and Northrend into her service. Perhaps it's the war, and not Pandaria, that will bring these two back.
Of course, there's other things to consider. For all we know, Alleria hunts Turalyon's killers through the Twisting Nether, stalking demons on countless Legion occupied worlds. It's a big universe, and we simply don't know where these two are in it.