Im optimistic that with such projects, and the evolution of the political process along with governance in this country, that such issues will resolve themselves over time. Accountability is improving in Pak, people are more aware of the issues.
But none of this will happen without economic development and empowerment. Mass transit is step toward both. It is as essential as electricity is to the far flung villages. Im sure you understand the importance of such projects to the development of the nations cities, and the central role that large cities play in growth.
All I can say is, give it time. Pakistan’s problem isnt one of corruption so much as it is about instability. The lack of a stable political environment creates the environment in which corruption and institutional weakness can thrive. Let the system evolve and function. Over time, the wrinkles will be ironed out. India is considered stable not for lack of corruption, but for democratic institutions, built over successive decades which create at least a modicum of political stability and thus growth.