I agree the instructor makes the biggest difference. However, PADI, which I am part of as well, does have a pathway for recreational divers. The apex of this path is "Master Scuba Diver". My open water cert is NAUI and everything else is PADI. From my experiences PADI is more strict about adhering to standards in a class. Each Instructor has a set of standards to teach from and deviation is not tolerated. Therefore, when a PADI professional looks at certification levels/cards there is an expectation and comfort level that you know the card holder has met. PADI also certifies more divers and professionals than the others.
In all fairness I can not discuss NAUI nor SSI as I am not familiar enough with their pathways, standards, or processes.