Do you want loose ends/unanswered questions that might hint at any theme or just time travel?
I'm going to list some things from each, but I'm forgetful right now so forgive me if some of my lists are bare. It doesn't mean that ones I remembered more hints for are more likely.
For time travel, we have the fact that 5.4 promoted the Timewalkers from an excuse for the card game to explore past Warcraft games to full canon:
- We have the fact that a new type of "Timewalker" instance was added in the 5.4 files, but is not currently announced as a feature.
- The Timeless Isle, despite being off the coast of Pandaria, really came out of left field for both the audience and the characters. It doesn't seem to currently be particularly relevant to the Pandaria plot, but Kairoz is having you do stuff on the island in order to research what he fears might become an upcoming calamity.
For Burning Legion, we have:
- Wrathion warning of an upcoming reckoning with an image of Azeroth being attacked by what appeared to be infernals.
- The Blank Scroll short story showing that if Garrosh wins, the Burning Legion would be ready to sweep over what's left.
For Azshara:
- Mentions of horrors rising from the sea after Garrosh's victory in the Blank Scroll story.
- The massive loose ends from Cataclysm.
- The fact that she's one of the last remaining, established major villains.
Other:
- Varian has vowed to clear the plague in Gilneas and resettle it, while Sylvanas, right next door, has outright stated that she will not follow Vol'jin.
- The Kor'kron that were watching the Undercity to make sure Sylvanas will not try anything have been killed.
- Blizzard has mentioned that various factions have noticed that Sylvanas is becoming more and more like the Lich King every day.
Things I intentionally left out:
- Alleria and Turalyon's Return - We may very well need them to confront what's coming next expansion, but no one ever said what that was. Alleria and Turalyon are heroes of one major thing: fighting the Horde during the Second War. They went missing under circumstances we're still not aware of sometime between Warcraft II and Burning Crusade. We have no proof they even fought any major Legion force outside of demons summoned by the Horde. All we know is that they're heroes. They could be helping us with pretty much anything. Their mysterious disappearance could have been because we go back in time and bring them forward because of something that happens soon, they could have entered a portal that took them under the seas of Azeroth, or they really could have taken the fight to the Legion in the Nether and Argus. We have no idea at the moment.