Well, its odd how a thread starts one way and then somehow ends up where it was not intended to end up in. So without further ado, lets derail it some more.
The thing about the whole debate over which of the recent Fallouts is the better one is..a bit odd to say the least, mainly because it is really about personal taste and consistency. I prefer New Vegas for two reasons, and I will go into detail a little further down. The first reason is that Fallout 3 was a clusterfuck of so epic proportions that I am still not entirely sure how it became popular, even though I am glad it did or New Vegas wouldnt exist probably. The second reason is that New Vegas is much more consistent in tone and plot with the first two.
The reasons for those two points are simple. Fallout 3 has a very basic plot, it is interesting, but it suffers from the problem the game in general has. All the side quests are very basic "Go here, find X, decide whether to be an ass or a saint", so we got black and white morality right from the start, which isnt a good thing. The bigger problem however is the railroading plot. You have no choice but to look for your Dad, you dont, you can dick around in the wasteland forever, shoot raiders and so forth, but the mainplot is "Go find Pops" and the writing and handling of it is terrible. You dont have a choice to even find him because you are mad at him, the perfect example is the initial dialogue with Three-Dog, all the choices come down to "Please help me find my daddy", there is not even the option to be more direct or hostile towards him, or imply that you hate your dad. Everything in the game's main quest is basicly "You love your dad", hence we have lack of basic choice, we have no option to specify why we want to find him, or even a choice to say "screw him". The plot wont advance unless you do exactly as told. The only real choice you get in the game, aside from the aforementioned side quest choices, is whether you want to put the FEV into the water or not, again either be the devil or be a saint with no middle ground.
But the biggest of all the problems with Fallout 3 is essentially that the timeline is wrong. Everything about the presentation implies that the bombs dropped recently and my belief is that initially the idea was that it was only 20 or 30 years since the bombs dropped. But that was changed for a simple reason, to allow Bethesda to rehash familiar content. If the game was set 20 or 30 years after the great war, we would have no Brotherhood, we would have no Super Mutants, even the Ghouls are somewhat unlikely since their existance hinges upon very specific circumstances (read up on the Bakersfield Vault, or Necropolis Vault). So without either of the two bigger factions, Super Mutants and Brotherhood, you have no definite good guy faction. 30 Years after the great war, the Brotherhood, even if they managed to get to DC would be colossal assholes, think the Outcasts just worse. The problem there is that Bethesda did not really create a new story on their own, they simply used known factions and content to craft a story that internally does not mesh very well.
Those are to me the biggest issues that Fallout 3 had, and while i would not say its a bad game, it is subpar due to it when it could have been a greater game. I also wouldnt say that New Vegas is without flaws, but it is consistent with its own internal lore as well as the lore of the previous games.