Neither I or anyone else I am aware of said lines would "basically disappear." They would move steadily, which they do not currently do. The aggregate lines in a park would fall because guests wouldn't be waiting in two lines virtually as they are waiting in another physically - crowds in stores, restaurants, and public areas would also fall. Lines would not be standardized over the day - they would fluctuate in length from morning to night, and less popular rides wouldn't have their waits artificially inflated.
Again, THIS IS THE ONLY WAY THE PARKS WERE DESIGNED TO WORK. Parks designed for line-skipping would look very different - they would have more attraction capacity, much larger public areas, restaurants, and shops, more locations for seating, more street performers and scheduled shows, and more things to explore in each land. For line-skipping to work, the parks would need to be redesigned from the ground up.