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.
As far as my own preference, I'm really hoping to see the Fall of Stormwind to the Orcs as a mission. Many players seem to have only joined for Warcraft III at the earliest, and most do not read the novels or comics, and may not understand how deep the Alliance and Horde rivalry truly goes, and what battles happened in the distant past that have created the type of atmosphere of growing distrust and anger than has only been exacerbated by the events at Wrathgate.
For me, I'd love to see an instance that begins in the Stormwind Throne Room where Garona has just assassinated Llane in front of his sons' eyes. Then we would have to lead Varian out of the castle and through the streets of Stormwind and to Anduin Lothar, who is directing the retreat of the civilians and preparing for the march north to Lordaeron. It would be a great way to get some background on the Horde vs. Alliance thing that promises to heat up even more in Cataclysm, and allow the Alliance to get some quality time with some of their greatest heroes, especially the lion himself, Lothar.
World of Warcraft: Cataclysm will destroy Azeroth as we know it. Nothing will be the same. In WoW.com's Guide to Cataclysm you can find out everything you need to know about WoW's third expansion. From Goblins and Worgens to Mastery and Guild changes, it's all there for your cataclysmic enjoyment.