First off, everyone knows the Commonwealth is based in pre-war Massachusetts. I picture the setting to be something like this or maybe somehting smaller (image taken from Google Maps) (http://img11.imageshack.us/i/commonwealth.jpg/
second, some locales...maybe places like the John Hancock Tower and the Prudential Tower could be included (or something that goes with the divergence of the fallout timeline, something representing such locales in spirit)...MIT definitely has to be included, because that to me seems like it could a big focal point for the Commonwealth and the Institute. Maybe its the Institute's headquarters, where they create their Androids. Maybe it's the head of a local government trying to rebuild itself, which leads to my next point.
Third, I imagine some kind of government in place, like locally run. Something along the lines of NCR, but on a smaller scale. A struggle perhaps between this government and the Institute.
Again, its all speculation, but speculation is always fun.