I keep thinking that there was some voice line that Three Dog had to respond to me about blowing up the citadel, but I spent hours in DC again to try and hear it from him, to nothing.
I then went up to Three Dog himself, after quietly assassinating the Brotherhood group that was hostile to my prescence there, only to have Three Dog call me the Hero of the Wasteland returning.
Like...what? Was the poisoning the world not enough? Was the whole killing the Powered Armored "good Guys" not enough either to get a reaction out of him? Where's the reaction? Where's the logic behind him handing me the key and coordinates to an armory so I can keep killing more of the people who protect him?
One thing that I do enjoy about Fallout 3's storyline, which is also well and featured in Vegas, is the ability to skip forward in bits. I don't have to inquire through beagle as to where and what Benny was doing, and the same goes for Moriarty(I also vaporized him, so eh). Then I don't have to go Meet Dr Li or go to Project Purity and look for him, and I don't need to go to Novac and talk to Manny(couldn't kill Dr Li, but Manny's skull is in several spots scattered about Novac).
So I go to Smith Casey's Garage and I head into Vegas. Very sort of similiar in that regard, but the fact of the matter is that Vegas features many many many more options on how to proceed towards the end goal at Hoover Dam than the fight to the Jefferson Memorial, and one of the nicer things I enjoy is the simple lack of scripted events that I hate. that plot device grenade in Vault 87 agitates me so much as compared to the taking of the chip from me in Caesar's Camp at the fort. It also didn't degenerate into me fighting through Powered Armor(as a slick smooth talking altruistic bastard of a character to rival benny, this was me being a square peg jammed into a triangle hole).
The choices between Vegas and 3 are of a much greater variety and depth. Fallout 3 was so damned Binary between what amounts to the options that a White Leg would pick, or what a young, romantic Ranger would pick.
But sometimes Fallout 3 kind of gets it, and its what makes these games so odd is that they made made with so many different visions at once. The Pitt, The Brotherhood Outcasts, and Harold all come to mind.
The Pitt is a good DLC because it sort of touches on questions of how to recover, methods, and means to an end. I can never tell if Ashur will deliver on giving the cure to the Trog Mutation to the Workers of the Pitt, or if the slaves will actually be capable enough to defend themselves without the Bosses, much less work on the cure in a small corner of a blighted Steel Mill. What I don't like is that the end rewards are nearly the same, regardless of who is in charge, with the biggest difference being the survival of Ashur or not. It changes, but in a way that has less talked about than even Honest Hearts.
The Brotherhood Outcasts are almost like a moment of sentience for Fallout 3, where you have an actually legitimate and capable organization that is doing what it should be, with leadership, boundaries, and opinions. If only the other 80% of people in Fallout 3 were given the same level of treatment/unique look. Don't make them just raiders, slavers, or Tribals. If a character in New Vegas can admit to jokingly making up a tribe name for a single story with as many moral questions as a Fallout 3 DLC...
I really don't like that I dragged Harold across America just so they could root him in one spot, but the dilemma of a person wanting to die or not and how other people have visions for him and of him was not a bad little bit. This quest has so many different options on how to proceed, with some decent consequences, but I suppose some questions could appear, like why a member of the brotherhood outcasts would give you a suit of heavy power armor if you couldn't wear it(and he doesn't train you to wear it).
tl;dr I think the big reason I, and others like New Vegas' writing over Fallout 3 is that there is so much more of it, and it is so much deeper.