Yeah, Skyrim had the same problem with radiant quests often choosing the same location over and over. In F4 I've lost track of how many times I've been to Back Street Apparel. I feel that radiant quests should at least give prevalence to locations you haven't been to before.. but instead it often seems like it works the opposite way.
There's many places I've been to at least twice..These are ones I've been to more than twice.
Corvega Factory. 4 times
Back Street Apparel. I lost count but I'm going to say at least 5 times.
Saugus Ironworks. 3 times. (had to kill the "leader" every time.)
Mass Bay Medical Clinic. 3 times.
What I especially find annoying is that all these places they send you back to are "cleared" areas. Once you get a quest to go back they respawn with exactly the same enemies in exactly the same places. To me, if it says cleared, it should stay cleared. I don't care if there's a quest that leads you back there. Just stay cleared. I shouldn't have to re-clear it.