Any problems Boston has, or has had is the fault of very poor city planning decades ago. The Big Dig has had a tremendous effect on the traffic in and around Boston making things a lot easier. However, things could be even better. The fundamental flaw I see in the planning for streets and highways in Boston starts and ends with the idiots who decided against the grid system and decided to put the heart of downtown on the akward and odd shaped tip of Boston that it is located on. Add in the fact that the current expressway/ highway system we have in place today is inferior to those of other cities, and we have problems.
I was out in Chicago the other day and one thing I noticed they do, along with Los Angeles, is have traffic lights at highway on ramps, and also a temporary extended entry lane from each onramp onto the highway, something Boston needs.