First off, I would argue that PADI (used only because it was used above, most agencies are the same) is not the Harvard of diving, but the State University system of diving. A good, standard education system, where you will receive a good standard education, but nothing fancy. I would then argue that a degree from Harvard is more valuable than a degree from a state education system not for what you learn, but for who you meet, and the contacts you make. If you don't understand this, it becomes most apparent in your late 40's when you want to break the $250,000 dollar a year salary barrier.
Second, I would argue that any student rating system is flawed from the very definition. If a student likes a professor, it's probably because, while they may have learned something, they liked them because they weren't challenged in the class. IMO, University isn't where you go to get educated on a topic, although admittedly I never attended a regular matriculated 4 year school (although I have more than one Bachelor's degree), University is where you go to learn to handle the day to day BS of the next 35 years of mind-numbing slave wages. That includes putting up with the bad bosses and the bad coworkers and the bad work situations and the bad spouses. As well as the good spouses and the good bosses, etc. So a program highly rated by the students is probably worthless. Likewise, dive training that doesn't challenge every student individually to excel, while teaching something, is not an excellent system.
I say that the instructor is the only person who can challenge a student. A system that requires mastery of skills, which is the majority of systems, while allowing 8 students to be taught by one instructor, is adequate, but does no favors to the student. This, by the way is most programs. I single out no one. It is the State University way, adequate but nothing special, and reasonably priced. But if you want to be an excellent diver, you must seek out those few instructors that probably won't even take you, because you won't appreciate their efforts. Those few instructors tend to gravitate towards more esoteric training agencies, the Ivy Leagues, if you will, of scuba education. Sure, some stay with their state universities and just do an outstanding job, but they have a hard time, as the training agency may only allow mastery of a skill and not excellence. Some students are only capable of scraping by. Should they be denied an education? Not at all, but they need an instructor who can teach each student individually to their capability.
So, it's the instructor AND the agency. But I do wholeheartedly agree witht he premise laid out in the OP.