Structured content is when you create content types and fields to model the content for your site. You define the fields needed to capture and represent the data on your site. For example, an event would have date and location fields.
In contrast, embedded content would be stuff you can put into a WYSIWYG box. Anything the toolbar allows you to add like tables and images or whatever else is configured.
Two different strategies for allowing content flexibility is adding more components that allow for structured content or working with systems that give more options for embedding content.
I think the field is moving toward structured content, although there are many slick embedded content systems available. Structured content can easily be reused, but can be harder to configure since you're stringing together parts of a system. Embedded content can be more flexible for content authors, but tricky to build complex systems or enforce consistency.l