Subway: I think the subway should connect the main districts of the city, like the rich districts, the commercial areas, and the slums. It could be a fast way to travel between different places, and maybe certain lines could be more dangerous (for example, near criminal areas) or blocked off depending on quests or events.
Bus: I think buses could be used for certain quests or specific factions. For example, there could be a special bus that transports illegal goods, and players could choose to intercept it, or work with the people who run the bus to gather info.
