I think their choice of JSON-LD as the recommended format and not being transparent in how it effects results is the biggest issue. JSON-LD requires duplication of content, where as microdata is inline with existing content.
Microdata used to be the recommended format. Google eventually switched recommendations to JSON-LD, and I updated my tools to reflect that.
JSON-LD is far easier to work with. Having to mix metadata with markup was a pain. Half the required elements would have to be hidden in CSS because they didn't make sense in context.
JSON-LD is also much easier to generate in scenarios where you can access post meta data and output scripts but can't necessarily filter HTML markup output (WordPress, corporate CMS, etc.).
A lot of websites are now generated using static site generators and it is much easier doing so inline, than have to duplicate the content which also makes the pages much bigger. Like I said the issue is more about lack of transparency about how it may effect ranking.
