The article does hint on some interesting points, but I disagree with it overall. The Air Force has to utilize aircraft to fulfill a number of different missions:
-Stealth penetration
-Air Superiority and Long Range Patrol
-Ground Attack / Heavy Bombing
-Electronic Warfare
-Search and Rescue, Transport, etc.
Depending on the aircraft utilized, these roles can overlap. For instance, an F-16 can fulfill both a ground attack and air superiority role, but it doesn't match the B1B at bombing (obviously) and it certainly can't match the F-22 or F-15E at air superiority, but for most missions it does an extremely good job. What has made the US Air Force so extremely effective and dominant worldwide over the last 30 years is its effectiveness at stealth penetration, electronic warfare, and air superiority. If the enemy can't fight back, then what does it matter what aircraft is dropping the bombs? The F-35 is actually going to be an extremely good aircraft once it's finalized, because unlike other aircraft, it's centered around an extremely advanced avionics package that allows it to collect massive amounts of data and intelligence, spot and target enemy radar, and pick out objects on the ground that other planes could never see. It's also, according to former F-16 pilots, a pretty decent dog fighter, but that's not going to be its primary mission; the US Air Force flies F-22's and F-15's on interceptor missions simultaneously while the ground attack airplanes are doing their job.
Overall I think the F-35 will be a fantastic plane once it goes fully online. It's been sticky, for sure, but it's going to replace many different aircraft that already need replacing anyways, and it's going to simplify the logistics chain dramatically, which is always a plus. And since our allies will also be using it, it will simplify the logistics chain with them, too. Ever consider other nations flying their warplanes on our ships? Currently only the French Rafale-M is capable and licensed to launch from a US carrier, but imagine the British being able to fly and launch from our 10 Amphibious Warfare ships as well. It brings a lot of new possibilities to work with our allies.