Fallout 3 Pros
* More evocative settings: Megaton, Rivet City, Tranquility Lane, The Capital Ruins, the Capital Wasteland, and Vault-101 are all highly different and diverse environments for adventuring in.
* The greater sense of danger: Everything is trying to kill you in F3. The subway levels, especially, felt like they were claustrophobic and filled with all manner of horrible ghouls. The ghouls actually felt menacing then.
* Three Dog: As much as he got to annoy me by harping on the SINGLE quest I did one thing bad (I swear - after Tenpenny Towers - it was the only story he played); he was a much more vividly realized character than Mister New Vegas.
* John Henry Eden: He was, indeed, an extremely likable character. Malcolm MacDowel's performance was just awesome.
* Better Music: I just think it was a slight edge. "I don't want to set the world on fire", "Crazy for you", "Butcher Pete", and so on are just more enjoyable for me while I really only enjoy "Big Iron on his Hip" by contrast.
* Broken Steel: I confess, it had to be mentioned.
* Apartment themes: I loved these and thought they made your homes much more interesting. The Presidential Suite doesn't remotely suit MY Courier while I hate Novac, so I can't even say that's the sort of place I'd want to live. While Megaton's house was just MY home.
New Vegas Pros
* More Likable Companions: As much as I liked Fawkes, the companions in Fallout 3 were all fairly one note. Veronica, Boone, and Cass all have more personality than all of the other ones put together.
Who even WAS Star Paladin Cross?
* The Politics: NCR, Caesar's Legion, Mister House, and so on all gave interesting views about how society functions on the West Coast.
* The Wild West theme: I really enjoy Westerns, so this was really enjoys.
* The De-Fanging of the Brotherhood: I felt the games treatment of the BOS went a long way to showing the flaws of the organization and how they weren't the setting's Jedi Knighthood.
* The Length: I felt there was much more to DO in New Vegas than the Capital Wasteland and am getting more bang for my buck, even Pre-DLC.
* More interesting sidequests: A lot of times many of the places you visit don't have much to do but there's a more intimate set of sidequests, I think.
* The Villains: Caesar, Mister House, and Benny have stiff competition in Von Braun and JHE but the fact is that Benny is someone you dog for HALF the game tirelessly. That made his death MUCH MUCH more satisfying.