My impression is that project overages have scared cities quite a bit. To use your Boston example, the Big Dig certainly has scared many other municipalities thinking of something like that. The Denver Airport fiasco most certainly scared away people from building new airports for decades.

Moving into speculation... I believe that society values lives a lot more. It would be very hard to cost effectively build another Golden Gate Bridge due to the lives involved. Is this really a bad thing? So instead we build skyscrapers.