People who think any new air traffic control system is going to help airport congestion are most likely going to be disappointed. While the author's talking points seem pretty unassailable, I personally don't think his solutions automatically follow. Rationing (and let's face it, that is what he's talking about) never works in the long run.
Congestion is the automatic result of demand exceeding supply. To reduce demand, increase the cost of the supply. This can be done negatively via "congestion pricing" landing and takeoff fees, and positively by providing "off-peak" fee discounts. These prices would provide clear signals to consumers, who would adjust their travel plans (and airline schedules) accordingly. The profits generated could be large enough to provide the funding required to fight off the lawsuits which are the main impediment to airport expansion. New runways means more capacity, which causes the price to drop, and now you have a positive feedback loop that's self-sustaining.
That's how it should happen. But we all know, if it happened at all, it wouldn't be easy. Most US airlines are too poorly run to understand such an arrangement, let alone take advantage of it. Anti-market luddites on the left would start shrieking about "limousine runways" denied to "the poor." Statists, who see government regulation's hammer as the tool useful for any nail presented, would refuse to even consider something that didn't provide more government jobs at taxpayer expense.
And so we'd end up with a problem that is, well, the problem we have today. Still, there are incentives being applied. Congestion and the resulting delays provide their own form of increased price, causing customer dissatisfaction, which takes business from airlines and airports who participate in booking shenanigans and gives it to those who don't. Does it decrease safety? Perhaps, but, considering the always-improving safety record of air travel, not by very much and never the same way twice. Does it increase the stress of everyone involved? Absolutely. Markets are almost always stressful places in which to work, but they most definitely do work, and pretty well at that.
Saying "updating air traffic control software won't solve airport congestion" is a real and valid point. Coming to the conclusion that the only workable fix is increased government regulation and imposed rationing is, in my opinion, unwarranted and most definitely counter-productive.