Fallout 3:
*D.C was much more interesting to explore than New Vegas was. Much of New Vegas was an empty desert which can get boring at times, while D.C had you crawling through the irradiated ruins of the capital of the former most powerful nation on Earth. *Fallout 3 had a better post-apocalyptic feel to it, everything felt desolate and that people were struggling to just get by.

*John Henry Eden was written very well, the Enclave were painted as American Nazis and the way he spoke and the speeches he gave always filled me with a sense of patriotic pride. I knew they were evil, but I didn't care, I would follow that man to hell and back. Also the twist that he was actually a computer was pretty cool. "Hey, kid I'm a computer! Stop all the downloading"

Fallout: New Vegas
* Better Characters * Better Factions * Main quest was actually interesting * Weapon modding and crafting * Better DLCs

So yes New Vegas was a better game overall, which is amazing considering it was made in only 8 months compared to Fallout 3's 4 years of development time. Holy shit Obsidian really can work miracles. But, BUT, more quests does not necessarily mean a better game. Yes it's cool to have more quests and more interactions with factions but if those fewer quests are more interesting then the the upside of more quests is rendered null.

TL;DR Fallout 3 had a better setting/environment, but New Vegas was a better game overall. (Also, I still can't figure out how to make blank lines in order to break up sentences)