I've been getting along fine using JSON for pretty much everything. That being said XML has some very sophisticated features like rigorous schema definition, a query language, a formal include syntax, comments (that's a big one), it's a lot easier to do multi-line content and in fact you can mix normal text and structured data.
The include syntax doesn't get enough love. It's crazy that JSON doesn't support it.
The issue with all the XML sophistication is that essentially only environment where all that really works is when you use XML as a markup language for technical publishing (ie. DocBook, DITA, ...) and in fact as a less convenient but more modern and cool SGML replacement.
Random applications that read XML just aren’t going to implement fully validating parsers, because it is lot of completely unnecessary work. Also in the article mentioned pattern of storing everything in attributes mostly comes from the fact that working with CDATA nodes in XML is major PITA wrt. whitespace handling and coalescing adjacent nodes.
The include syntax doesn't get enough love. It's crazy that JSON doesn't support it.