I think the biggest difference is the funding environment. In a way, it's a networks effect problem.
There are consumer Internet companies that made it big in the valley, in the process, creating millionaires who "get" consumer Internet. They then go on to create or fund other consumer Internet companies.
Meanwhile, in Boston, there hasn't been a significant consumer Internet exit.. at all? (Wow, I can't think of one right now) So the promising consumer Internet businesses and talent in Boston, who can't find the seed funding or the mentorship, move out to the valley.
What I see in SV is a lot of hype, douchebaggery, and exploration of the business model space with light agile startups. What I see in Boston is more academia- and government-connected activity, and high, high technology. Stuff that requires greater capital investment and time to develop a market. Both have their advantages and drawbacks, but if you like things like robotics or Lisp, you're probably better suited in the Boston area than SV.