A Fallout "New Britain" err mod would be interesting, but as indicated the fallout series takes place in the US and there are TONS of places and I do mean TONS of places to venture into. Personally I would want to see something done in New York City course with 911 happening and all that might be in bad taste even though it happened more than 8 years ago. Maybe something in the Sunshine state down in Miami or something in Arkansas or Alabama. Some may not believe it, but there's a lot of stuff in Alabama including an old rocket test area. My mom's father (my grandpa) worked for a company that made solid rocket boosters for NASA.
Ney York shouldn't be in bad taste. Hell, if anything, it could be a sort of respect.
Besides, the WTC wasnt designed till 1960, and wasnt constructed till 66, and completed in 1970, so it wouldn't be pat of the Fallout world really. Plus, it is already implied that millions, if not billions of people died in the war, so having the WTC at all IMHO wouldn't be disrespectful.
Perhaps it could even be the focus of the Ney York area? Home to most inhabitance as the main "city". lol That actually sounds rather interesting. An urban wasteland with 2 towers standing tall among the rubble, filled with life, and center of the new age in the area.