Though we must also consider, that Fallout 3's timeline is fairly inconsistent with the Original Fallout's. Since after all, by this point(on the West Coast), the NCR and depending on your choices during Fallout 2 other cities etc. are growing and expanding into the Southwest. I always found it odd, that the East Coast seemed so devoid of life and settlements, to be honest it never made much sense.
I tend to agree, which is why I wish they had set FO3 earlier then they did. I'm also hoping New Vegas is set earlier. I like Fallout best when the world is still messed up.
That said, you can kind of make it work when you think about how FO Tactics (which is treated at least partially as canon by FO3) presents the midwest as still being pretty chaotic even after the events of Fallout 2. Probably the best way to think about it is to assume that the west coast is recovering faster and the east coast is slower. Civilization is moving west to east.
On the other hand, there are hints in FO3 that maybe things weren't so bad the whole time since the war and that there has been a relapse. After all, Vault 101 was open at one point and then closed. The adventures of "Daring" Dashwood refer to locations and other incidents that no longer exist, not to mention the implications of his story being turned into radio plays. It all suggests the possibility that things were improving and then went backwards.