THROUGH ROUTING. The Overhead Wire suggests that's a good idea for Boston commuter trains.

In Boston specifically, the North and South Stations are not connected but a run through would likely make the system more efficient in my eyes. It would allow those on the North a one seat ride to places of work in the South and vise versa. Think about the way the Septa system does it, running trains through downtown to the other side of the city, all connecting at the central station.

That's an old idea (post is titled Going Through Boston) with current support. It's also one that will be hampered by previous downsizings (post is Once The World's Largest Terminus) particularly at South Station.