To me the biggest issue is how empty the map is. There's almost no signs of human habitation. You'd think there'd be more than a few half-intact suburbs, but nope. New Vegas on the other hand did a pretty good job of showing how built-up metropolitan areas are. There's water pumps, substations, half-intact burbs on the outskirts, industrial and tech areas... Meanwhile in FO3 you have... D.C. and Megaton, and then a few random whatevers dotted around that are just there because it seems like the developers just felt like that place needed a few burned-down houses. It says something that the fucking Nevada desert has more signs of habitation, both past and present, than the fucking D.C. area.
I think at least some of that might be chalked up to the fact that DC got hit a lot harder by the bombs. I mean, the white house is a massively radioactive crater, meanwhile Mr. House managed to use lasers built into the Lucky 38 and computer networks with broadcast capability to either disarm or shoot down all but 9 of the 77 nukes fired at the Vegas area, and none hit the city itself.
I doubt a gambling city like Las Vegas would be as high of a priority target as Washington DC which is the seat of our government power. The Chinese wanted that place fucking gone, and for the most part they got it.
Then you have the fact that DC is just plain nastier. There's more of everything everywhere. More raiders, more ghouls, more deathclaws, mirelurks, a huge army of marauding super mutants, etc. DC is an absolutely lawless wasteland outside of a few areas. For all New Vegas' talk about how unsafe the roads were there are really only a few places that get super dangerous, and some stretches of road with not a lot on them at all except some coyotes or easily avoided powder gangers. Fallout 3 often just threw shit at you.
Oh hey, having fun out there crawling around the broken landscape? Have a deathclaw!
Also probably hard to found a settlement when you have raiders trying to rape, kill, and rob you, slavers trying to haul you to The Pitt, and Super mutants hauling everyone off to become more muties or food.
One thing that kind of sucked about New Vegas, as realistic as it was, was how much nothing there was in it between locations. Like that dry lake near Nipton that had fuck all on it except a burned out car with a suitcase in the back and a toolbox. The only thing there at all was a few radscorpions and some ants, and a few sparse pickable plants.
Also, there were areas that could be considered inhabited, tho some are random encounters. I was constantly finding places where scavengers had holed up, usually with a dog.
Then there were Megaton, Tenpenny Tower, Rivet City, Arefu, Girdershade (which was just 2 people, to be fair), the subway inhabited by The Family, Reilly's Rangers compound in the DC ruins, Canterbury Commons, the Citadel, Big Town, Little Lamplight, Paradise Falls, Oasis, the Temple of the Union, Underworld, Greyditch (though its been destroyed by the time you get there), Vault 101, and of course all the fucking Raider and Talon Company camps goddamn everywhere like Evergreen Mills. Place gets even more inhabited once the Enclave shows up and starts setting up outposts.
I honestly never felt like the place lacked human inhabitants, just that they were very spread out.