The rapid transit built in New York beginning with the first els codified two characteristics that spread to the rest of the US, and are often seen in other countries’ rapid transit networks as well. First, it is separate from surface transit – even when it did still have grade crossings, they were controlled railroad crossings, rather than street-running segments as is common on light rail. And second, it is separate from mainline rail.
Not much later than New York started building els, Berlin built the Stadtbahn, also an urban elevated railroad. However, it was meant to be used for mainline rail from the start, with two local passenger tracks and two long-distance passenger and freight tracks. Part of the impetus was to connect different railroad terminals within the city, which American cities did by building union stations disconnected from local traffic. Shortly later, Tokyo built its own mainline rapid transit system – the Yamanote Line bypass in 1885 and Tokyo Station connecting the Chuo and Tokaido lines in 1914. Both cities ran frequent local commuter service early, Berlin doing so even before electrification.
Of course, nowadays US regulations locked in the separation of rapid transit from commuter rail, but at the time, there was no such separation. New York could have built its subway to mainline specifications and run trains through to the LIRR. It didn’t because of historical accidents – it preferred compatibility with the els and even when the BRT chose a wider loading gauge for its own subway network, it still opted for narrower trains than on mainline track. At the time it seemed like no big deal, although some of the subway lines built were redundant with existing commuter lines (for example, the Flushing Line with the Port Washington Line). Again due to historical practice, commuter rail did not try to operate to rapid transit standards, keeping frequency low, and so nearly all urban stations closed. In both New York and Chicago, it’s often easy to figure out where the city ends or where the subway/L network ends because that’s the point beyond which commuter train stop spacing narrows, providing makeshift local service.
In subsequent decades, the German and Japanese approach proved itself much more capable of providing good transit to growing suburbs. In Tokyo, subways are legally railroads, and most lines are compatible with at least one commuter line in order to permit through-service. German cities have mainline rapid transit (S-Bahn) and also separate subways or subway-light rail combinations (both called U-Bahn). Many other cities and countries had to adopt the same system to increase transit ridership, at much higher cost since the necessary viaducts and tunnels connecting stub-end terminals were done much later. This is what led to the Paris RER, and what’s led to Thameslink and now Crossrail in London. Any other approach would require spending even more money on extending urban lines to the suburbs, exactly what’s done now in the two big suburban-focused US rapid transit systems, the Washington Metro and BART.
The kink is that despite the above problems of subways that are separate from both mainline and street rail, there’s now a different reason to build such lines after all: they can be made driverless. Most first-world cities already have legacy rapid transit or else have so much sprawl rapid transit is inappropriate, and third-world cities aren’t saving much money by eliminating drivers, but in the few cases of new builds (Vancouver, Dubai, Copenhagen, the newer lines in Singapore), driverless trains are common, and this allows trains to run more frequently, or even 24/7 in Copenhagen’s case.
This kink aside, there’s really no reason for a city to build a new New York-style subway, i.e. disconnected from light and commuter rail and running with a driver. Extending a legacy system is fine, but for new systems, there’s no point. This could be especially bad in growing third-world cities, which could find themselves paying too much for a subway they don’t need or unable to connect a subway they do need to the suburbs once they start suburbanizing. Third-world construction costs aren’t much if at all lower than first-world costs, but wages are much lower.
Some of the world’s largest cities have made or are making this mistake. Mumbai is building a new subway, on a different track gauge from the Indian mainline network, preventing through-service to the overburdened commuter trains. Shanghai and Beijing have vast subway networks, without express tracks or any ability for trains to run fast through city center; they have widely spaced stops so that they are faster than most other subway systems, but they have nothing on the rapid commuter trains in Tokyo. (Beijing is also developing a parallel commuter rail network, running diesel trains from the exurbs to the traditional city terminals at low frequency.) It works fine now, but when Shanghai grows and suburbanizes to the degree Tokyo has, it may find itself having to spend many billions on digging new tunnels.
Since a New York-style subway is inappropriate for new builds, some cities need to ask themselves which of the three kinds is the most appropriate. A subway-surface solution is mainly an option when one underground line can naturally split into multiple surface lines, as is the case in Boston, San Francisco, Cologne, and Frankfurt; this is because there’s a big difference between on-street and grade-separated capacity.
Tel Aviv, which is building a subway-surface line without any branching, is doing it wrong. For the other choice, I believe it’s a matter of how well-developed the suburban rail network is, and how much future suburbanization the city can realistically expect. In Tel Aviv specifically there’s also a separate element, which is that for religious reasons public transit does not run on weekend. If driverless technology makes the difference between trains that run 24/7 and trains that run 16/6, then it should be used even at the cost of otherwise worse service to some suburbs and destinations easily reached by legacy rail branches.
Finally, in North America, one of the reasons to engage in strong regulatory reform is to allow the mainline option to work. Some lines, for example the Harbor Subdivision between LAX and Union Station, should ideally host a mixture of local and rapid trains on the same tracks, and also allow intercity trains; if the Harbor Sub becomes an electrified commuter line then high-speed trains could serve the airport, providing a connection from the Central Valley to a major airport in addition to SFO, which would only get a station at Millbrae.
More in general, the only real disadvantage of legacy commuter networks is that they tend to not be very dense in the center of the city, requiring new builds; most of the Tokyo subway is just lines offering the commuter lines more capacity into the CBD, overlaying itself to also provide a tight in-city network. There’s no technical reason not to just build an electrified local mainline network as its transportation backbone, and if more capacity is required then build additional lines in the mold of Tokyo.