Which is why I was surprised to read this post over on Mystic Chicanery. They argue that the Caverns of Time are actually the most "real" of all the instances in the game. If we go into Utgarde Pinnacle, for example, and murder King Ymiron, there's no reason why he should be in there again the next time we head in. And yet he is -- we can go in and murder him time and time again, doing the same thing, and getting loot every single time. But in CoT, there's a logical explanation for why the instances are always the same: to the people we're encountering in the instances, it's the first time we've met them. From the outside world, the CoT instances may seem strange (the first time I was in Durnholde, we wiped with Thrall, and I jokingly checked with my guild to see if Thrall was still standing in Orgrimmar, alive and well -- he was), but inside the continuity of those instances, they work.
Of course, we do still get different loot from it every time, as the MC post notices. But it is quite a thought: even though the Caverns of Time instances are the ones in the game that seem to least need us messing around in there, they also might just be the most logical.