Looks like the Charlestown roadway is getting the same treatment as the Forest Hills overpass: The city announced today it's going for the surface-road approach rather than an underpass:
"In partnership with the Charlestown community, we're working to transform Rutherford Avenue from a highway to a neighborhood-friendly, urban boulevard," Mayor Thomas M. Menino said. "Residents will be able to take advantage of new connections to the MBTA Orange Line, new greenspace for children to play, and safe access to the Charles River. The new Rutherford Avenue will offer these and countless other opportunities to enhance quality of life for the people of Charlestown."
NorthEndWaterfront.com has more, including a discussion of whether the proposal will mean more traffic in the North End.