Philadelphia is the same way. New York on the other hand is more of a spaghetti mess. I wonder if that interconnection does things for the city too, like encourage growth in more areas.
Not really. Look at the map again. Everything flows through Manhattan. The entire system is setup to take you to Manhattan. If you want to go from the Bronx to Queens or Brooklyn, you go through Manhattan.
There's really only one line for which this isn't true: the G from Queens to Brooklyn.
Lines like the M [0] that could fairly easily have been designed as a full circle, are actually U-shaped, because it's really about funneling people in and out of Manhattan.
London is a bit like this as well, most of the trains that come in from Outer London are commuter trains that go to a ring of termini around the centre, then you have to change onto the Underground.
They're trying to tackle it at the moment by setting up new lines that go through the centre, but start and end far out regionally, so to go north to south you don't have to interchange from one terminus to another. Thameslink and Crossrail are both part of this concept. The model comes from Paris, which has the RER network, separate from the subway.