It makes more sense if you interpret the extremely low population numbers displayed onscreen as canonical.
The baseball stadium shantytown has 85 people in it and they don't seem to be having kids. The only conclusion is everyone is nearly sterile, so population sizes are so extremely low that cleaning up entire destroyed cities is basically impossible.
Though uh, nature should have destroyed a lot more stuff. This only makes sense if nuclear winter also reduced basically all weather.
And those cities are lucky that high level creatures like Deathclaws tend to mind their own business in their territory because holy shit if an endgame Deathclaw wandered into Boston it would fuggin solo Diamond City
I don’t know the lore of FO4 but since it’s post apocalypse wouldn’t there be roaming bandits and splintered factions which would make unification and community planning difficult?
If the reason for the bombing was due to government bullshit then people would likely be very reluctant to form larger communities.