Complaints about Prolog are nothing new, but this is a recent one (is anything in the gripes something we haven’t seen before?) by someone who’s writing a book Logic for Programmers (which I haven’t yet read).
I wonder if I should here in this thread reply in substance to the article you shared.
All gripes are valid, and each of them has been resolved in at least one way; the author does not yet know about it. But is it really worth it to go addressing each one individually?
Instead, I will use this forum to tell you my biggest gripe with SWI-Prolog: it does not have an authoritative exhaustive tutorial on its website. I am certain that the authoritative, exhaustive Python tutorial that lives at python.org was a major enabler for early adoption.
A good tutorial provides context, guidance, motivation of choices, best practices, in other words, does all the hand-holding that a novice requires. It is also, by definition, strongly opinionated. This is what makes it so difficult to write well.