You may as well ask "Do you prefer post apocalyptic sci-fi or high fantasy?" since the two universes aren't really comparable in the same way as say, Tolkien and WarCraft, or Warhammer 40k and StarCraft.
I expect the majority of responses will be talking about Oblivion (with a few references to Morrowind and even fewer to Daggerfall/Arena) and Fallout 3/New Vegas (with a few references to Fallout 1+2 and even fewer to the non-numbered Fallout games) as opposed to commentaries on the universes as a whole as representatives of their chosen genre.
For the record, from what little of Fallout 1+2 I've played (I REALLY need to get round to those) and the playthroughs of 3, New Vegas, Morrowind, Oblivion and a teensy bit of Daggerfall? I prefer Fallout. It sticks out to me as something different. There's a lot of high-fantasy universes - a lot of them done well, but there are precious few good post apocalyptic universes (not games, universes) that are in depth and truly interesting to read about.
However, I freely admit on both counts that my view is based on incomplete information.