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The filesystem is super confusing to tons of users. The reason people put crap all over their desktops is because they "lose" it if they put it anywhere else, while the desktop always stays "where it is". I don't think anyone's come up with a good solution to that problem, yet (Apple's isn't very good, and Windows' similar moves with its defaults aren't any better) and we're far enough into computers being common tha…
Believe it or not, the way the filesystem worked on the original Mac operating system was that things did stay where you put them. Open a disk and the folders on it could be put anywhere in that 2D space, and each folder's contents could similarly be anywhere in their virtual 2D space, and each disk/folder opened in its own window that even re-opened in exactly the same position with exactly the same size as when you…
Relatedly, IMO iOS took a huge step backwards in UX when iOS7 moved away from a highly spatial interaction metaphor for practically the entire OS—by which I don't mean the skeuomorphism, exactly, but things like folders sliding the screen "open" when tapped, so that they had a sense of physical location within the main screen. Or "slide to unlock" looking like a physical slider so you didn't even need to read it to know what to do. The loss of the security blanket that was the physical (or at least faux-physical) home button has hurt it, too.