> tree-like file systems, multiple users, access privileges,
Why should everything pretend to be a 1970s minicomputer shared by multiple users connected via teletypes?
If there's one good idea in Unix-like systems that should be preserved, IMHO it's independent processes, possibly written in different languages, communicating with each other through file handles. These processes should be isolated from each other, and from access to arbitrary files and devices. But there should be a single privileged process, the "shell" (whether command line, TUI, or GUI), that is responsible for coordinating it all, by launching and passing handles to files/pipes to any other process, under control of the user.
Could be done by typing file names, or selecting from a drop-down list, or by drag-and-drop. Other program arguments should be defined in some standard format so that e.g. a text based shell could auto-complete them like in VMS, and a graphical one could build a dialog box from the definition.
I don't want to fiddle with permissions or user accounts, ever. It's my computer, and it should do what I tell it to, whether that's opening a text document in my home directory, or writing a disk image to the USB stick I just plugged in. Or even passing full control of some device to a VM running another operating system that has the appropriate drivers installed.
But it should all be controlled by the user. Normal programs of course shouldn't be able to open "/dev/sdb", but neither should they be able to open "/home/foo/bar.txt". Outside of the program's own private directory, the only way to access anything should be via handles passed from the launching process, or some other standard protocol.
And get rid of "everything is text". For a computer, parsing text is like for a human to read a book over the phone, with an illiterate person on the other end who can only describe the shape of each letter one by one. Every system-level language should support structs, and those are like telepathy in comparison. But no, that's scaaaary, hackers will overflow your buffers to turn your computer into a bomb and blow you to kingdom come! Yeah, not like there's ever been any vulnerability in text parsers, right? Making sure every special shell character is properly escaped is so easy! Sed and awk are the ideal way to manipulate structured data!