One underrated difference between countries is how multi-tracked railroad junctions look. In France, double-tracked regional lines have grade-separated junctions that ensure no crossing oncoming traffic. For a plethora of examples, consult the RER track map and look at any bifurcation. Looking at Google Earth, the same is true near Tokyo. This is standard rapid transit practice anywhere I know of, and Paris and Tokyo both treat their regional rail systems like urban rapid transit.
In the US, this is not true. Even important, high-traffic mainline junctions are often flat – see for examples the Main Line-Hempstead Line junction on the LIRR (Queens Interlocking), and the Hudson-Harlem junction on Metro-North (Mo Interlocking). The major junctions involving the Northeast Corridor tend to be better, fortunately. Harold, the LIRR/NEC junction, is already grade-separated from oncoming traffic, and the current grade-separation project is only for same-direction traffic; and the junctions in New Jersey are grade-separated. The Kearny Connection splits the problem in half – it is grade-separated for NEC trains but requires Morris and Essex trains in opposite directions to cross each other at grade. However, even for NEC trains a few major problems remain, most notably Shell Interlocking between the Northeast Corridor and Metro-North in New Rochelle.
I suspect the problem is that double-tracked lines in the US are not consistently thought of as having one line in each direction. The arrival of centralized traffic control (CTC) has made wrong-direction running easy; some railroads ripped their second tracks, and the commuter lines that remained double-tracked freely run trains wrong-way during weekends or (as is the case on the Worcester Line) when there are freight trains on the line. At a few places, four-tracked segments on running track connect to two tracks in nonstandard ways: for example, at Providence Station, three of the four platform tracks merge into the southbound running track. The concept of having one track per direction and no crossing oncoming traffic, which is standard on the subway, doesn’t really apply to commuter rail, leading to scheduling problems.
In New York, there’s no alternative to grade-separating the worst junctions, including Mo, Queens, the Kearny Connection, and the unnamed Far Rockaway/Long Beach and Ronkonkoma/Port Jefferson junctions. Although frequent train service exists with flat junctions, the schedule is irregular and unreliable, and has few reverse-peak trains. Fortunately, this is a problem for commuter trains more than for intercity trains, for which schedule adherence is more important.
In Boston, the NEC itself has flat junctions at all of its branches. Fortunately, there are alternatives to concrete. The Franklin/Providence junction requires Franklin Line trains merging onto the NEC to cross oncoming Providence Line trains at grade, but lets them continue onto the Fairmount Line without conflict. Since the Fairmount Line is getting some investment and more frequency is under discussion, having additional trains serve the line is a net benefit, and all Franklin Line trains should go through Fairmount. The Needham Line branches at-grade, at a more constrained location, but there are plans to connect it to the Orange Line anyway, and much of its geography is suitable for subway service more than for a regional rail branch. This leaves the Stoughton Line, for which there’s no alternative, but fortunately Canton Junction is not a very constrained location and the junction is simple.