I'm guessing that Wrathion will go back to old Draenor with the help of Garrosh, the bronze dragonflight traitor and the hourglass (stolen) to try to unite an army strong enough to defeat the Legion in the coming war. We will follow him back in time in order to prevent the unravelling of history.
1. Both the Alliance and Horde are weaker than they were at the start of the expansion, and time is running out. At this point Wrathion is obviously very desperate to find a way to prepare the world, and neither the Alliance or Horde are viable options after the events of SoO. What other armies are near strong enough to be prepared for the legion in the current timeline?
2. The Timewalkers flashforward, where we see Anduin speaking to a prisoned Garrosh. Many people think this is a disguised Wrathion, and I tend to agree. Perhaps it was the only way he could get some alone time with Garrosh without creating suspicion?
3. I can easily see Wrathion attempting to completely destroy the current timeline in hopes of preventing the oncoming war. His moral compass is clearly quite warped, considering he orchestrated the extermination of his entire dragonflight, then immediately began to pit two superpowers against each other in hopes of inspiring a genocide. If he perceives something as being for the "greater good", he has shown that he has no issues doing anything required to do it. We are just pawns to him, and after the events of MoP and SoO we've been taken off the chessboard in Wrathion's eyes.
Wrathion: To do what is right, no matter the cost. That is wisdom.
Yu'lon: But true wisdom comes from KNOWING what is right. And sometimes, DOING nothing at all.
Wrathion: When is it ever wise not to act for the greater good?
Wrathion: I promise you this. I will stop at nothing to prepare this world for the battle to come.
Wrathion: I will leave nothing to chance.
Wrathion: NOTHING!
Wrathion: A divided Azeroth cannot possibly stand against the darkness.
Wrathion: The Burning Legion WILL find Azeroth. Seas of blood, cities in ruins! Who are we - one divided world - to stand against a legion? You speak of hope. Believe me, the thinnest silver of belief that we might somehow survive the coming devastation is all that sustains me.
4. Many of you have mentioned that it makes no sense for us to travel back in time and mess with the timeways, and I agree. There's no way that Blizzard would have our characters do something so morally uncomfortable, not to mention something that would completely destroy the lore of the game. This is why the goal of the expansion will be to prevent Wrathion from doing so. Obviously with time travel nothing will end up exactly how it was initially, but it's the difference between minor lore changes and the entire history of Warcraft being re-written.