The company best positioned to handle Amazon, Sears, was parted out and gutted by its chairman and CEO Eddie Lampert. Toys "R" Us had a working business model and were gutted by VC's. So I wouldn't say they were quietly laying down, they were actively raided for their accumulated wealth and this left them unable to compete.
Best Buy is probably best example of a company that figured out how to pivot and survive. They basically turned into consumer electronics consultants that tell people what to buy to solve their problem (at a gigantic markup). Amazon.com can't compete with that model as it's not built for the consumer that doesn't know what they want/need to solve a problem (or are afraid of knockoffs).