Not really sure what they have to do with Roger's "legacy" - at least on the surface, anyway.
JJ's problems began with his knee injury, much like Julio's blip when he got hit with that comebacker against the Mutts. Neither likely had much to do with McDowell's throwing program or "tough love approach".
I'm certainly not qualified enough to decide if they could be exactly the same, but I think 2014 was a lot like what happened with the Mutts this year - a perfect storm where a collection of great young Pitchers all went down at once. Coincidence? Maybe, maybe not. However, if enough evidence is eventually found that places that blame at Roger's feet, my guess is that Warthen will probably be blamed for what happened with Harvey, deGrom, and Matz in 2016.
I'm afraid the bigger issue here is that really good Pitching Coaches are all going to become dinosaurs soon, because they're going to have to be replaced with medical gurus. The fact that specialization has become so prevalent and these guys aren't trained to go more than 80-90 pitches renders the strategies involved with getting through a lineup even a third or (God forbid) fourth time useless. "Go cut it loose for 90 pitches and we'll finish it for you" has more or less become the rule, and I'm afraid the few "Aces" in the game today are likely going to be the last ones.
Sour grapes? Sure, to an extent. The thing is, I think a lot of people are going to find that this is going to be one of those areas where they wish the game didn't evolve in the long run. I'm not sure you can reverse this course now that it has started. When "Aces" are guys that can get through a lineup twice without allowing more than three runs, there aren't going to be many "heroes" on the mound any more. The fact that "Quality Starts" dictate a Pitcher's value as much (or more) than Wins or ERA will eventually change the game completely, and I'm not personally convinced it's going to be for the better.
One thing that has become pretty obvious though - you can't bring all these young Pitchers through the minors being developed following the new standards and then hand them to old-school guys when they get to the show - the approaches rarely jibe.