The problem is that most of my pages don't have any parent. I need them that way so that they have shorter URLs (like example.com/page-name) which are easier to remember. For my clients this is preferable. Then I arrange the pages in the nav menu according to the hierarchy I want them to have, where it makes more sense for them to be located in the drop-down menu structure.
I'm not aware of any other way of accomplishing this, other than leaving the pages without any parent - but that means the breadcrumbs don't work, because they don't match the menu hierarchy which is the hierarchy the end-user sees.
So in fact I am logically organising my content - but I'm doing that on the Menu page, rather than via the Pages section of WordPress.