A lot of it was fair criticism at the time. Linux fixed some of what was wrong. Having a good sudo config mostly resolves the problem of having one superuser account, and big, multiuser systems are a lot less common now, anyway. X's network transparency features aren't that useful in modern computing contexts, either, though I have found a few over the years.

But mostly, it's because the landscape changed from a hundred Unix vendors vs a bunch of other OSen, to now where it's Windows vs Linux vs OSX. By that comparison, the two with Unix-derived history look well thought out.

(This also implies that NextStep was the one old Unix vendor that has survived in a meaningful way. I don't think anyone would have guessed that 30 years ago.)