First of all the arguments against realism:
There is no agriculture in FO3! (No it's not as if the frequent Brahmin farms count. As if the limited agriculture in New Vegas is any more realistic. And hunting is obviously the main source of food for people in DC which makes perfect sense.)
Iron sights are an unfair advantage. (How the hell is something that is realistically part of the firearm an unfair advantage?)
Radiation isn't enough of a problem. (A complaint I've heard for both games, people don't seem to consider it has been over two centuries since the bombs fell. That aside, I don't think it appeals to the main stream to have to constantly manage radiation.)
Storyline wise:
Obsidian/Bethesda is better at writing than Obsidian/Bethesda (This is purely a matter of opinion, I personally found the storyline of FO3 more interesting while I have encountered more characters I appreciated in FNV. It is noteworthy that in the reviews I have read, particularly the gamespot review, FNV was marked down for having an unappealing storyline.)
The Storyline of FO3 is good/bad FNV is more gray. (While there are more grayish options like siding with Mr.House, as it stands the game is still presented very much in a NCR good CL bad manner. It could be argued that the storyline of FO3 is somewhat gray as well because the Enclave's end goal is actually better for the human race in the far long run. And the Brotherhood can be seen to commit it's share of evils like the slaughter of innocent ghouls and the massacre at Megaton.)
Theme:
Fallout: New Vegas lacks the tongue-in-cheek clever sarcasm of the series. (If you look for it you'll find it and sometimes you don't even have to really look. If there is anything that is consistent throughout the series it is the somewhat sarcastic and satirical view of the past. Or at least, clever quips here and there throughout the game world.)
Fallout: New Vegas lacks the 40s/50s feel that people enjoyed in the past. (It's set in [censored] Vegas with Frank Sinatra blaring half the day.)
Other:
Fans of the originals all hated FO3 and liked New Vegas better. (This is easily the most [censored] argument of them all since it is an example of some trying to speak for all. I personally know someone who is a big fan of the originals and hates FNV.)
More reasonable arguments:
Fallout: New Vegas is extremely unstable. (This is true for the vast majority of people I have spoken to, and for myself. However as I continue to play the game obviously, I have confidence that the problems will be fixed with time.)
Fallout 3 doesn't follow the series very well. (I've played the originals and I realize this, but I really enjoyed Fallout 3 and I think in the end it captured the same civil-apocalyptic theme if not a little overboard in the apocalyptic area. And nothing makes it any less Fallout 3.)
Fallout: New Vegas doesn't allow you to play after the MQ. (True, and with so much to do with the MQ aside, I dislike this fact. Whether or not they will 'fix' this is a matter of speculation. I personally doubt it.)
Fallout: New Vegas isn't very evil friendly. (In many ways it isn't, but this is true of a vast majority of game unfortunately.)
Fallout 3's companions were very removed from the story. (This is true and In my opinion followers are one of the few areas in which New Vegas makes a vast improvement. Although I still miss Fawkes.)
Fallout 3 was too easy. (I personally found Fallout 3 more difficult at least early on than New Vegas. Then again my jack-of-all trades build is designed for all situations. I don't specialize.)
There, I have addressed the issues that matter most to me. Feel free to add your own as long as you can address them in a sensible manner.