The road bike is slower because drop handlebars are ********. I suppose that they are great for long journeys and spandex geeks who spin at 500rpm, but in stop-and-go traffic, you need wide handlebars (and/or a rohloff speedhub) to get yourself up to speed with the cars.
Your best bet in commuting is wide, no-drop TT bars, with barend shifters and brake levers on the bottom. If you have a steel frame and 25+ width tires, you can mash right into the potholes--just get off the saddle for a second.
Yet more blasphemy: Biopace chainrings are GREAT for city.