In the mainframe world, TOPS-10/20 and VMS were both exemplary. From the user POV, the former was one of the best command-line systems ever created, with none of the insane user-hostility built into UNIX command naming. Dave "VMS -> NT" Cutler absolutely hated Unix, and it shows.
But we're really comparing cinder blocks and potatoes. UNIX was designed as a hobby/student hacker tool, not as a general user OS. Many of the design choices are bizarre and frankly stupid, as the book delights in pointing out. But hackers love UNIX because using it just it feels just like hacking code, and that's considered a good thing.
It wouldn't be impossible to design an OS with powerful command line options but a sensible command naming system, much more intelligent and reliable security, a modern filesystem, and so on - and perhaps add some of the user configurability and extendability of the Lisp/Smalltalk/Hypercard(?) world.
But UNIX is so embedded now it would be a purely academic exercise.