Couple of observations, neither pro or against:
If cave-dwelling NPCs would alert others in the cave, you will eventually be over-matched by a number of NPCs and you wouldn't be able to finish the dungeon. Also, it doesn't make sense to have the first enemy you see run inside the cave yelling for help:I've never played a game where enemies run away from you.
As for dungeons telling a story: there could be some sort of quests associated with certain dungeons, and there were many of those in Oblivion, plus I am guessing there will be quests involving dungeons in Skyrim, but just randomizing many different activities for dungeon dwellers on non-quest dungeons doesn't make much sense, as you are not going to be spending that much time inside a dungeon observing NPCs and frankly, there's no much to do in a cave.
In Fallout, given the setting, there was a lot more variation in the settings and themes in the dungeons: you had military locations, newspaper buildings, bottling companies, car dealerships, power plants, etc.. so there was more material to work with as far as dungeon theme and story. In a game like Skyrim, there's caves and old castles
and there's just so much you can do in a cave.