For cities that are more advanced in transit connectivity, bigger plans are taking shape on how to connect regional rail systems. That is, making commuter rail connections such as the tunnel that would connect the Eastern and Western rail terminals under the Danube River in Budapest. This connection would connect subway and tram systems with existing regional systems much more intuitively. It's something I think a number of US cities should start thinking about including San Francisco and Boston.
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.
As for San Francisco, it would be nice to see the second tube, where Caltrain could go to somewhere like Richmond and Martinez directly. Anyway, it's an interesting thought. But it also brings up a point that Paz made on the issue of sprawl and commuter rail. Though in my opinion, this is an issue of neighborhood design, such that people can walk to the grocery store, elementary school and other activities.