I liked both. But really they are both in a very different setting.
Fallout 3 was set in Washington DC which was the epi-centre for all the chinese nukes, and that's why you mainly go through the DC ruins. You come across alot of nuke related stuff like ghouls and mutants. I hated going through subway after subway, It really got really annoying & repetitive.
Fallout New Vegas was set in Nevada, Las Vegas,(also called New Vegas ingame) a place mostly untouched by the atomic warfare thanks to a person called Mr.House. So you don't really find as much ruins,(it's a desert mainly anyway, for the most part).and less nuke related creatures. But in this game, you get to meet a whole lot of a new different factions, including the original brotherhood of steel. It's really fun as well, and any Fallout fan should give it a shot.