I wonder why Boston hasn't risen further, with Harvard and MIT both at their doorstep along with a lot of other really great universities and good companies.
There are lots of places with a wealth of well educated talent and poor to non-existent amount of startups coming from there. Access to capital is probably the largest factor.
Boston is doing pretty well and many things started in Boston such as YC, Facebook, Dropbox, etc. Boston is small and already expensive. Plus the weather. I also think it doesn't have a lot to offer for single people. It has much more to offer for families.
Boston is also more diverse in terms of opportunities. If you're a researcher or biologist let's say, you are more likely to find a good job in Boston than SF.
Stanford was unique in the aspect of students being encouraged to take their research and make companies out of it. The vast majority of universities are not as selfless.