Not defending the FAA...
But understand that since it was established (after some horrible collision over the Grand Canyon by two airliners sight-seeing in the 1950s) the FAA has had a confusing mission...
Promote commercial air transport
... and ...
Keep ALL air operations safe
From my read I don't think that this mission statement was the issue. It sounds like a procedural issue that wasn't followed. That to me is a management issue between an operator and his regulator and not an industry wide problem.