I was thinking that if it comes down to of maybe giving it a crash site... or *the* crash site and making a quest similar to S27's Dalek where you can help it only to have it go... well... dalek on you and the wastes. An enemy almost immune to bullets and totally unphased by energy weapons, killable only by exceptionally lucky sustained fire on the eyepiece or huge use of explosives would certainly be a memorable encounter. Sure, the 'bullet melting' ability of a dalek is a post Mccoy addition but even in their last old school outing they were basically totally unphased by human firearms.
Another story line that might be quite intresting to persue would be to have the darleks chained up/inactive/imprisoned in a locked, sealed cell in the citadel. the idea being of course that the united states government found and imprisoned them in the pentagon before the 'great war' and they've simply layen their rusting for a while.
Obviosly the brotherhoodof steel can't know about them, perhaps the player would have to stumble onto them, kind of like an easter egg?
And the reaosns for them eing imprisoned? it seems before the war technology was MUCH more advanced than the technology on earth during dotor who, perhaps before alot of knowledge was lost in the great war we had weapons capable of incapacitating even a darlek?
One of the amazing things about all this is the FO3 World could easily be an alternatedimensional version of earth, much like the one Rose fled to in doctor who, only, well different of course.