Hmmm. My brother is NAUI certified and the family and I are PADI. Never noticed any difference, except the card. I think we went our own ways based on what was offered locally. I WILL say this, if you are planning to take your certification dives in another location (it was Hawaii for me, the Caribbean for hubby and daughter, and the Great Barrier Reef for the other daughter ), I would call ahead and get your cert based on the the company you will be doing the dives with; it will be easier than the reverse. Once you are certified, I don't really think it matters, as long as you have a card (and a log with some places).

Robin

edited for clarification