Perhaps, I'm putting too much faith in Bethesda, but they give me the impression that there was another game in Fallout 3 that was scrapped and replaced with the material we got from the main release. I don't know game design, so what I assume (and yes, it is a big assumption) is that world design came first before quest and story design. Maybe the release date they set for themselves prevented them from really making sure the material they used was at least somewhat coherent.
It really does seem that Fallout 3 was to take place just a few dozen years after the war occurred. Somewhere along the line, they thought that by adding in the BOS, the Enclave, and the supermutants, it would be a fallback to that classic Fallout feeling. However, this is impossible to have happened in this early lore time frame and to make it work, they moved the timeline a few hundred years forward. Of course, this makes no sense given how rushed the events where, but the designers have already admitted they will sacrifice sense to make something cool.
The entire world just screams right after the war. It wouldn't surprise me if the world Beth had built was near completion before they started to add in things like quests and the main storyline. They really didn't have a preplanning outline and the whole experience just feels like a "Fuck it, let's wing it" session. I even remember reading somewhere that with Oblivion, Todd really didn't have the time or means (or talent) to do much predesign before they tackled the game itself. Which yet again, gave that game a very amateur messy feeling.