This is tough. I really enjoyed both games. However, I think F03 was more "Doom and Gloom", you emerge from the vault having never set foot in the world before and everything is ruined, there's people out there dying or starving and there's raider and other factions killing or eating people. I was actually blown away by the world and what was going on in it, I suppose it played with my imagination a little because I really got into my character.
New Vegas on the other hand, everything is not as depressing, the world is starting to develop a little more and people seem to be doing pretty well. I think I like New Vegas more because of all the crazy things you get to do and see, I also liked how I was able to see a destroyed Washington D.C.
I almost feel like playing both again.