Fallout 3
Pros: Immersive, enjoyable, more believable story, ripe for its time, fun DLC, expansive world, great voice acting, fluid mechanics, fewer but stronger quests.
Cons: No companions, limited weapons, glitches, too few actors.
New Vegas
Pros: Better start, more voice actors, bigger world, whole new environment, many more quests, many more quest-paths, half-decent companion system.
Cons: Crashes, bugs, dodgy voice acting, choppy animations, obvious breaks in environments meshes & textures, empty world, bugs, crashes, outdated engine, boring expansion packs, borderline lame storyline, more loading than playing, crashes, bugs, crashes, bugs, despite being made by the makers of F1&"2, fits into the cannon worse than F3.
I'm vote goes to F3 being better. I actually had fun and got immersed in it. all I saw in NV was bugs, glitches, broken quests, breaks in floor textures on the desert floor...
If you gave F3 way more diversity in its main quest, it would have been the best game ever. Fallout New Vegas just got dull for me quickly, plus the fact that every time I started to get immersed, something would happen to drag me back into reality. that never happened in F3.