it is even more expensive in parts of Boston known for having the worst problems. The Green Line (which isn't even analyzed) runs through Back Bay, which is largely landfill[1] without very good engineering properties. Combine this with running under many buildings that are National Historic Landmarks[2][3][4] and have shown shifting with bits of construction such as adding an elevator[5], these tunnels are pretty much impossible to expand.
[1] http://www.bc.edu/bc_org/avp/cas/fnart/fa267/boston/bos1820.... [2] http://en.wikipedia.org/wiki/Boston_Public_Library,_McKim_Bu... [3] http://en.wikipedia.org/wiki/Old_South_Church_in_Boston [4] http://en.wikipedia.org/wiki/Trinity_Church,_Boston [5] http://www.boston.com/news/local/massachusetts/articles/2008...
I'm not at all familiar with Boston, but I know a fair bit about DC and the main issue is pretty straightforward - tunneling is monstrously expensive.
Combine that with a lack of dedicated funding and the competing interests of DC / MD / VA for what funding there is you'll hear 'premature optimization' faster than an HN thread suggesting a three tiers for a startup web site.
That's before you consider that the system is shallow enough near the center to run alongside anything with three or more basement levels and the fallibility of switch gear.