Exactly, I have thought the same thing myself. Seattle metro area, LA, NYC, Atlanta and others, should get status as a State. Allow CA, NY, GA, MI and Illinois to separate from the jungle gyms that are the major cities.
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.