The recent Twitter dev chat confirmed what is fast becoming a tradition: We will be getting a new Caverns of Time instance with the upcoming expansion. It's certainly not something I have much trouble with. The Caverns of Time are an excellent tool for looking back and understanding old pieces of the story that brought us to the current world as it is. Unfortunately, the devs were not willing to drop any hints as to the exact nature of the new instance, but we can, of course, make our own guesses.
The original questioner suggests War of the Ancients as a possible destination. In a way, that might be an interesting battle. It would, if nothing else, give us some insight into the character of Malfurion Stormrage, who promises to be a key figure in the expansion. That said, Rhonin, Broxigar, and Krasus have already traveled back in time to deal with the War of the Ancients, and you'd have to think that if you keep shoveling more time travelers back there, something's bound to give.