I have been certified diver since 1985, I am a SSI and NAUI instructor and have been a dive master on quite a few PADI classes, the bottom line, is you need to find a local store, and shop around if you can for your classes and gear, to get the best service.
When it comes to the difference with the organizations,it is in the core curricula, NAUI gives a huge amount of latitude to their instructors. A good example is dive tables; PADI only allows using PADI books and Materials, and PADI tables. NAUI instructors, can use any supplemental material they chose and most do. NAUL allows the instructor to teach the PADI, NAUI, and the US Navy Tables. As a NAUI instructor, I can use any current reference materials that I chose; with PADI I can only use PADI books or reference materials. This has both advantages and disadvantages for the store and instructor, your local Dive Shop or instructor, can make the best decision for there area and market.
Booth agencies have minimal standards that are very close, just a little different way to manage their instructors.
Also the bottom line for any professional instructor should never, put down or “dog” another store agency or instructor, The completion is not the other store or agency but other sports…. Talk bad about another sport not diving!