The whole idea of trying to talk about which city's mass transit system is greenest in terms of emissions per passenger-mile is terribly flawed.
Just think of it in terms of cars. Driving 5 miles in a 20 mpg car takes a quarter of a gallon of gasoline. Driving 25 miles in a 45 mpg car takes over half a gallon. Being the guy with the 5 mile commute and the 20 mpg car is considerably greener than being the guy driving much further in his Prius. The point of intra-urban transportation networks—whether you're talking about the mass transit element or the private cars or bicycles or whatever—isn't to transport people arbitrary distances, it's to get people where they're going. Having trips that aren't very long isn't cheating, it's a great way to achieve efficiency.