I always play it in FPS mode - I just think it looks & plays better and I'm not a huge fan of TPS in general, there are some games that are great when played from a TPS view (i.e Splinter Cell), it's just that in my opinion, Fallout 3 plays a lot better from a first person view.
Also I thought that the game is/was supposed to be played in an FPS view - I'm sure i read that somewhere. So following on with that I also thought that the developers just put in the TPS view for the original Fallout players to have a quick muck about with.