Kudos to Stephenson for inventing a new word that sounds better than the original. Phyles are no different from cliques and suffer from the same problems that cliques do, from an unclear power structure to unwritten rules that are arbitrarily enforced by a capricious "royalty," and in-crowds and out-crowds.
Cliques are great for those inside and terrible for those outside (everyone else). That we have managed to diminish their importance in core pillars of societal function is one of modern civilization's greatest achievements. Going back would not be progress.