The article was definitely thought provoking, but there a couple assumptions in it that I think are not entirely correct.

First, I don't believe that fly fishing was historically invented for purposes of being deliberately challenging, or for leisure for that matter. I doubt that the Macedonians that Aelian saw fly fishing in the second century were fishing for leisure, but for food. Certainly James Baillie, who showed Stewart his spiders, wasn't fly fishing for leisure; he was fishing to support his family by supplying trout to hotels. When I was in in grad school, I didn't eat the last week or so before payday if I couldn't catch enough bluegills or crappie on my days off to fill the freezer. And I used a fly rod because it was the easiest way to do so.

There was a long history of using live mayflies for bait; making artificial ones was done for the convenience of not having to go out and catch some every time an angler wanted to fish. (Taking some of the challenge away, you could say.)

We perforce have to view the history the fly fishing through the eyes of those who wrote about it. And the people who were fishing just to eat didn't have the leisure time to write (if indeed they could write.) It's Dame Juliana (yes, I know, she didn't write the Treatyse, but some literate person did) Sir Charles Cotton, etc. They were fishing for their leisure, but that doesn't mean the majority of anglers weren't simply fishing to eat, and that fly fishing was a convenient means of doing so.

Secondly, it doesn't follow that just because we fly fish for leisure (and I think it's safe to say today most of do) that we're necessarily looking for a challenge. History would indicate that we're looking to make things as easy as possible. We don't forge our own hooks anymore, as the Treatyse taught to do nor fish with a rod not longer that six yards with a butt the thickness of your wrist (as Cotton pointed out, you could possibly get tired fishing all day with a longer rod), nor use horse hair line knotted to the end of the rod (not even tenkara fans use horse hair.) We don't have to soak gut leaders before we fish, nor rely on snelled flies, because we now have eyed hooks. Each advance in fly fishing has made it easier to catch fish and less of a "challenge."
And the dry fly wasn't invented for the sake of conservation; it was invented to catch fish during those times when a sunken fly wouldn't. It's a bit hypocritical to say that the challenge has to be exactly what it was whenever we started, that all the changes before that time were perfectly legitimate and none made since that time are. (As much I feel that way myself.)

The third assumption if that it's easier to catch fish with a nymph under an indicator. I seldom fish that way myself because I don't enjoy it and it seems to me to be too much like bait fishing, which I don't enjoy either. That doesn't mean it's not a challenge to fish in that manner. If I were to be truthful with myself, I would admit that among the reasons that I don't like indicator nymphing is because I'm not very good at it and tend to catch fewer fish. People who are good at it have developed a legitimate skill.

The final assumption is that simply trying to catch as many fish in a legal manner isn't a challenge in and of itself.

In spite of all that, hypocrite that I am, I find my challenge in fishing tackle and techniques that were around when I started out in 1963. I fish mostly cane and fiberglass rods, and try to limit myself to flies that existed back then. No beadheads, no indicators, no wooly buggers (although I think Russ Blessing invented the latter about that time), no foam (although I'll allow myself a beetle from time to time), no flash except tinsel. How I supposed to compare myself with the writers whom I read vociferously when I was a child if I'm playing a different game? (And let's do away with the DH rule in baseball. Hey, you kids, get off my yard.)

You know what? I still catch plenty of fish.