I don't have a clear vision of how I wish it were structured, but I would say that if the big cities were actually "states", then each big city would get two senators in congress, and at least one designated congressman. Not ideal.
I would like to see City States which would have less than expected political power. Living in the city may be desirable for some (to make money, to enjoy culture, etc.) but reaping political power should not be possible in a city. It should be an area of political weakness, not strength. Otherwise, the cities become the tail that wags the dog -- which is what we have now.
IDK how to do it, but the big cities hold too much power, and they exert it with Federal funds to bribe the constituents.