It would be great to have the option to organize bookmarks into folders.
I prefer to have only a few documents (Work, Personal, Ideas). I have bookmarked main parts of the Personal documents (e.g. Career, Admin, Health). Plus I have bookmarks for my workflow within a document (filter by dates, colors etc). This means I have several bookmarks, each related into logical groups.
If we have this, the choice of “many documents vs one mega-document” becomes purely a matter of taste. Now it is: Use many documents with neat folders (but less nice search experience for task management) or one mega-document with flat and thus messy bookmarks.
Maybe I have explained it in a confusing way. If I have one big file with everything, I will have lots of bookmarks to navigate this. Then, having folders to organize the bookmarks becomes very useful. It is the same use case for having folders instead of laying all the files in a flat manner.