The question when I was looking for some one to train my kids in scuba was who to trust the lives of my loved ones with. It was not a certifying agency that I was researching, but which instructors in my area had the best reputation for top quality training, and are known for producing safe divers.
While there are a few PADI and maybe NAUI choices somewhat near, by far the best reputation in our region is held by a PADI team nealy a 3 hr drive away. I did my research. I was satisfied with this group, not because of the name of the agency on their door, but because it is obvious that they care about the sport and the lives of those they teach. They go the extra mile, as the saying goes.
My teenagers' c' cards maybe "only" be PADI cards, and no better a card than some less well trained than they can also carry, but it was the safe training of my loved ones that mattered to me, and not the paper that they carry afterward.
Myself, I was originally certified by the "Y" program, and have since taken several PADI course including rescue, with this same team, to keep current, and sharpen old skills. Loyalty to any brand or belief system means very little to me, when compared with the final results.
All of the above is my opinion only, of course.