i think skyrim was a giant leap in these regards, compared to fo3, but even more to oblivion, that's where i got that effect the most (even more than in morrowind)
basically, the dungeons are made from kit pieces though, so a certain amount of repetition will likely be inevitable, but what made the improvement (from what i saw) is, where they'd neatly line up these pieces as supposed in oblivion, they'd mix them up, stick them through eachother and abuse them in zillions of other ways in skyrim, to the effect that, in some places, you can't tell the pieces even if you know them. and i don't see why they wouldn't go further down that road.
on the other hand though, i'd like to say: considering the count of available assets, it's far beyond awesome how much they acchieve with how little. like, there's less than 10 different rock cliffs in skyrim (etc, same for pretty much everything there is in the game). ever had the impression you'd ^"seen that cliff before"? i certainly hadn't, although, as a modder, i KNOW the pieces.
for the unique dungeons: there actually are a couple unique sets (in skyrim), for whatever reason though, many of them though never are used in an actual dungeon (but in places like high hrothgar, nightcaller temple and so on). still, there are unique dungeon places, with a strange talent of pretending they aren't: riften sewers for an example, unique set. or funky devices that are hidden away in places so remote nobody will likely ever see them, like that odd dwemer teleporting device in kagrenzel
for fo4 anyway, i have VERY high hopes, since it seems from the trailers we'll see a much higher amount of "exterior" interiors, meaning without a loading screen and a view to the actual outside, this could mean a huge leap for "dungeon" design, even more for fallout (places that are supposed to be destroyed, collapsed etc)