How are you going to play music you've added in the last three years, but not heard for a month, from the "Latin" genre, with two or more stars, using only the file system? With an iTunes smart playlist, it's trivial.
In Calibre it's trivial to sort the books by Title, Author, or (my self-defined and filled) Genre column.
How would you even start to manage photos in the file system? By name?
honest question: why would you ever like to do that?
I find calibre unusable because of these things. I just have one epub file and I want to read it. However, the damn program forces me to "initialize my library" and other bullshit.
Photos is actually an exception for me due to the personal nature of them. I group them in directories based on date ranges and events. I don't want to upload them to some webapp or cloud storage for privacy reasons.
BeOS actually solved this 20 years ago with its file system BFS. Haiku is an open source reimplementation of BeOS that recently progressed from (high quality) alpha releases to its first beta.