I've never heard of the Boyd Group, but their "analysis" is way off. Delays are most problematic at the terminal, not en-route. there are only so many runways, and no matter what you do to the en-route system, you're not going to have much more density of traffic on and off of the existing runways.
So who's to blame for the delays that start at the terminals? There is some government causation here, but it's not what you read in the article. Airlines have packed the schedules especially with more smaller aircraft. This consumes the *airport* or *runway* capacity especially at the airlines' peak morning and afternoon push. So how is it the gubmint's blame? If they auctioned off the peak slots and metered the arrivals and departures to what the system (runways) can absorb, then the delays would go away. Ticket prices would rise, but so be it - the current system has no market-clearing mechanism for a scarse resource.
While there are warts on the en-route ATC system, it is not the root of the problem.
Building some new airports would be nice too. Hard to do, I know, but we're crowding a lot of people through a very dated infrastructure.