In FO3, there was just the main storyline, there were no factions or anything of any real significance. The Wasteland revolved around the story.
My first play through, when I got to the point that the Enclave showed up, I was pretty underlevel, and the game started wrecking me consistently. Then (rather suddenly) I got to the end and was all "Ummmm, whiskey tango foxtrot Beth".
I imagine a lot of people were worried about something similar here. I know a lot of the Oblivion players initially got the MQ (in FO3) out of the way so they could go on to explore the world and do sidequests and so on at their leisure. The reality was a rude awakening for many of us. Thus the backlash and the Broken Steel continue playing after MQ DLC.
Although I voted undecided, and mentioned as much in my last post in this thread, I'll probably still run a character straight through the MQ to see how it effects the world before I settle in to something more relaxed, aimless wandering and so on (my preferred way to play). Paranoia I guess.