There's not a singular thing at fault.

Though there is nothing inherently free or decentralized about "PKI", and given your conflation of those concepts I suspect that you're not actually aware of where the lines are drawn from.

Certainly the decentralized nature of PGP adds some challenges to good usability.

However, a large number of the problems come from the PGP spec itself (some of which is defensible in a 20+ year old spec, but not in anything in a modern system) and from GPG's poor implementation.