Navigating file system via GUIs is slow, painful, and for me takes a ton of cognitive effort after a short amount of time of accumulating files. Coming up with a system for organizing files is kind of hard in itself. Reorganizing as the number of files outgrows the system is also painful.
And choosing a place to save a file is often the best time to start a reorganization. But if I save a file in a new location, having to switch apps and now go back to that same spot in the hierarchy and reorganize is painful.
I don't have a good solution, just complaints, unfortunately. But after ~50 years of GUIs and hierarchical file systems I'm surprised somebody more clever than me hasn't come up with a better solution.