Reminds me of how the Department of Transportation is all about moving as many cars as possible, and the bike programs and so on are marginalized and ignored. Perhaps there should be a Department of Bicycles. The argument against splitting those sorts of things, though, is that it would promote interdepartamental conflict, and the new departments would be quite small and weak. I really don't know enough about the city government to say which way is better.
I think an independent voice and structure is necessary when it becomes too small of a priority in the grand scheme of things. At least an independent body would have a direct voice to the Mayor's Office that doesn't get interupted by the Agency's Commissioner...let them compete and see who wins what resources.

Right now while it would be great to have a fully integrated Dept of Transportation that effectively balanced cars, mass transit, pedestrians and cyclists it seems like the DOT is really the department of moving automobiles through the city. And the Dept of Sanitation is really the department of moving trash around and out of the city...