There is absolutely many examples of "fatally flawed" instruction out there. My personal experience flying with pilots who were not doing well was the fact that invariably the problem was a lack of fundamental flying skills. By that I mean they could not recognize and hold the correct attitude for what ever maneuver they trying to fly, could not maintain coordinated flight and could not smoothly transition from one flight regime to another ( eg straight and level to climb). This was because they had never been properly taught ex 5 to 9 in the first place.
My solution in every case was to go back to the very basics and practice the foundation ex 5 to 9 flying skills until the student had mastered them.
It will take a very persuasive argument for someone to convince me that there is a better way to teach the basic hands and feet skills that under pin every part of flying, although I am genuinely open to new ideas.
Where there should be change in flight instruction in my opinion, is in the thinking part of flying. Traditional flight training is all about the mechanical skills, but what is missing is the pilot decision making and threat and error management soft skills. On the very first lesson I talk about "time in the tanks" as an introduction to pilot decision making and all of my ground briefs lead off with the learning what considerations are relevant before/during and after performing what ever maneuver we are going to do.