With the next patch being released in a few weeks, and having been confirmed that we learn who the next Warchief will be in the SoO closing cinematic, it has come to my attention as to who is most likely to be the new leader of the Horde.
Wrathion: But that idiot idiot, Wrynn, High King indeed. Why did he allow another Warchief, he could of united the world under the Alliance banner.
Lor'themar Theron says: Now, I look at our Warchief, and I begin to see the very same racism. He is willing to throw away our lives for his agenda.
Lor'themar Theron says: Know this: I won't stand idle if the Horde interests conflict with those of my people. I may reconsider old Alliances.
King Varian Wrynn says: I was trying to negotiate with the Sin'dorei. I was opening discussions to bring them into the Alliance! By attacking their people, you've forced their hand-
Right there it seems like this is the reason as to why Varian aloud a Warchief to be chosen. And it was stated that his choice will cause even more friction between him and Jaina, and by allowing a new Horde leader could do just the trick for such friction. And while I would expect Thrall to simply reclaim the title of Warchief, it seems like for some reason he has no say or is missing during the decision.