I completely agree with you. The main quest was possibly the least interesting part of FO3. What is your motivation for completing this quest anyway? Following in the footsteps of your father, who is so hung up on the project that he left abandoned you and stuffed up your comfortable life, leaving you alone in the wilderness? Whose only response to your finding him is "I need you to help me with the project"? I couldn't give a toss about his precious project. He kept insisting that it was urgent, but there was no actual urgency in the gameplay.

Finally your father completes his pattern of abandonment by dying in the name of his project. And of course everyone expects you to carry it on. I couldn't think of anything I wanted less. The rest of the world was a much more interesting place.

The final battle, as you say, was a complete anticlimax. I had been saving up my big guns for something major, and all I got to do was tag along behind Liberty Prime as it cut a swathe through the enemies ranks (although, I've got to say that the 50's jazz radio soundtrack made a delightful counterpoint to that battle.)

And the contrived moral decision at the end (still without any actual urgency -- you can go exploring for days without resolving the issue) well, as you say, it was disappointing.

In Fallout 1 the final narration was much better. It didn't talk about you, it talked about the long-term effects your actions had on the world, in various ways. I feel it gave a much better sense of closure.