I have worked on a lot of Amazon accounts and I even do a fair amount of retail arbitrage from TJ Maxx / JC Penney -> Amazon both online and in-store. Given that the bulk of my income either comes directly from Amazon sales or indirectly through consulting for Amazon sellers you would think that I would be in the ra-ra-ra-Amazon-will-annihilate-traditional-retail camp.
The big advantage that discount retailers like those have for shoppers over Amazon is price and being able to physically inspect merchandise before you buy it. The selection of certain brands is also often better at the physical retail stores.
The fact that you can make > 75% profit margins per unit in some categories flipping from discount retail to Amazon FBA demonstrates the advantage that these retailers have over Amazon. Amazon's fee structure also makes it so that certain price points are just about never going to be profitable for Amazon unless fees go down -- and fees have been going up quite substantially.
If you want good prices, you should not shop at Amazon - you should shop at a physical retailer.
So, Amazon has some issues with its model especially in categories like apparel that make it a pain to earn continual profits from. I prefer to sell men's to women's apparel for example because women return products for fit reasons at much higher rates as compared to men. Fitting measurements for women are also much less standardized because there's a lot of variance in female body shape. A return on Amazon is more costly to a seller than it is to a physical retailer.
Also, JC Penney generally has a minimum quality standard and often really impressive prices per unit that Amazon's fee structure makes it impossible to beat. You are not going to profit from selling a $7 polo shirt on Amazon unless the quality is awful and maybe if Amazon is buying it from you as a vendor. If you buy a $7 polo from JC Penney the quality might actually be great and JCP will earn a profit.
I have different opinions about Macy's because they generally do not have a price advantage. There is really no benefit to buying stuff at Macy's unless you really want the name brands and you don't mind paying a higher price. For a certain kind of shopper, that's what they want and that's what they'll get from Macy's.
This article is just as cherry picked as some of the 'death-of-the-mall' stories are. I could do a similar cherry picking locally by comparing one successful shopping complex about 30 miles distant from another one that is failing. Depending on which direction I drove I could tell a different speculative story about the future of the mall in small town America.
A lot of what is missed in the retail discussion is that while online retail is where a lot of the growth is, physical retail is where the bulk of the transactions still happen in the US. There is a limit to how much of that Amazon can 'eat.' Some if it is regulatory: in the latest issue of Total Retail, two of the biggest online sellers in 2016 were Walgreens and CVS. That's 'cause of online prescription pickup. If Amazon did go into that business -- as it might -- then the picture might start to look significantly different.