Build a railroad station at Route 95 & Route 128 intersection, with large parking garage [actually, there is a parking garage very close by, but it is hard to get to from Rt 95], and build train/subway line into Boston. People can then park their cars (after driving up Route 95, or on Route 128 from either direction) and ride on the train into Boston. This would relieve a large portion of the traffic at the 95/93 split, and on the southeastern expressway; as well as decrease the demand on parking in the city.
Build a “ring” railroad/subway along Route 128, with parking garages & stations at all the “spoke” highways that intersect with Route 128. Also, all of the existing train lines that come into Boston/Cambridge should have new stations where they intersect with this new “ring”railroad. People can drive (or bicycle, or walk) to these stations, and travel either along Route 128, or to another train station (Braintree, Route 95 (see above), Riverside, the Purple Lines, etc.) to travel in towards Boston.
This would relieve a large portion of the traffic on Route 128/95 and all roads from there in towards the city. It would be much more energy efficient, as well.