In the Fallout series it is often possible to skip entire portions of the main story via exploration or fast-talking someone. Apparently these shortcuts still exist in Fallout 3. However I stumbled on one that skips a chunk of the story, but does so in a very jarring way. You skip the portion of the story, but the dialogue doesn't change. It still assumes you've done and learned things that you haven't, and it makes the whole experience really awkward and unsatisfying. You feel like you've missed something, rather than just found an alternative path.
This happened to me, and while I don't mind the shortcuts in Fallout, I felt this one was poorly done, and it left me feeling "out of the loop" so to speak, giving me dialogue options to ask about stuff that I'd never even heard of before. I had to go back to an earlier save to reset the main quest.