I'll preface this by simply stating that I love both games for different reasons, which I have listed below.

Fallout 3
Strengths:

• More varied terrain.
  
• Dungeons. Dungeons. Dungeons. Places to actually go and get good use out of your fancy DLC weapons.
  
• More memorable sidequests.

Weaknesses:

• Rehashed FO1&FO2 story. After finding Dad I simply stopped caring.
  
• Boring unique weapons. Lackluster arsenal overall.
  
• Broken perks, and perks that didn't affect weapons they should have. (Pyromaniac and Demo Expert)
  
• Different Brotherhood of Steel that misleads a lot of new fans. For a new entry in an old series, this is bad.

New Vegas
Strengths:

• Infinitely superior main story. I was really interested in choosing a faction each of my Courier ideas would support.
  
• Vastly improved gameplay. Tweaked everything I didn't like about FO3.
  
• Better weaponry.
  
• Better/more Perks. Most of them actually worked!
  
• The real Brotherhood returns, and I was happy to destroy them on most characters.

Weaknesses:

• Needed more unique places and little touches in the wasteland.
  
• Zero dungeons. I was expecting a Mariposa-style military complex or the Dunwich Building.
  
• Less interesting side quests overall.

Agree/Disagree? Thoughts? Comments? Death threats?