Outstanding question. I am an OW instructor with SSI and with NAUI. The biggest difference is the methodology of the instructor as is "dictated" by the store. What do i mean by that. Some store owners stress safety more than others. Some ae more interested in getting your money than providing a good training experience. I know from my own experience that SSI and NAUI have institutional safety oversight over the store owners. PADI, I'm sure, has standards as well. One of the big differences is that SSI is the only agency that requires instructors to teach through one of the affiliated stores. This builds quality assurance right into the system. If an instructor isn't teaching the way the store owner wants, he lets them go. NAUI and PADI, the main two other agencies for recreational diving instruction, do not require working with a store. I could teach as a NAUI instructor out of my garage if I wanted. To me, that is worth a lot. But no matter how you look at it, the store management and the instructors are what make or break the experience. I've dived with people from certified by all different agencies. I've seen good ones and bad ones from any agency. I truly believe that the reason a person becomes a bad diver (i.e. unsafe) is really nothing at all to do with the certification agency. To toot my agencies horn, I feel that most of the SSI and NAUI divers I have seen are more consistently well trained.
For what its worth, there it is. Either way, I wish anyone reading this the best of luck. Remember to plan the dive and dive the plan. And perhaps more importantly, dive often and dive safe!!
Frank