(Note - I am not knocking FO3 overall.)
For example, for TES III: Morrowind, there is a mod named Julan Ashlander Companion. This NPC goes with you along the MQ and gives commentary in places that actually better explain some of the MQ decisions. Specifically, in one place the MQ sends you into an ancestral burial chamber to retrieve a tribal item with a very poorly designed motive. Julan explains it as "they don't expect you to succeed, but to die there and add you as tomb guardian - it's a trap." Basically the MQ is not changed, but the less well-thought out portions make more sense, both in and out of game in this mod.
So, has anyone done something like this for FO3?