I agree with you in principle, but in practice, when I was visiting New York in July, I got much better results by using an external app rather than Google Maps. ("NYC Subway", I think it was called.) Specifically, Google's directions often had multiple transfers and didn't mention any alternate routes, whereas the app gave me the route with fewest transfers and showed all the other lines going there, in case you missed the first train.
I think this is why Apple's plan to relegate public transport directions to external apps might be a good idea: there's no way a single company -- even one the size of even Google! -- can keep track of all the minutiae involved in planning routes for every public transport system around the world, whereas app makers can. Even today, every public transit system that I've been on has one or more apps, so I doubt uptake will be a problem. And with the new APIs in iOS6, it should be much easier to get directions via external apps, since they show up in a list right in the Maps app.
Oh, and the app worked offline, which as you might know is mighty helpful in large parts of the subway. :)