I went with NAUI just because it was the only one in the area. I suppose I would have done the same for PADI. However though I used NAUI, my other family members are PADI so I have seen both sides. I noticed NAUI is more aggressive. Maybe it was my instructor. They really put us through the ringer. Tide both regulators in a knot behind our take for example. I personally feel that what I had to go through allows me to take any emergemncy situation and deal with it ending with a good outcome with confidence.
Old school NAUI instructors can be a bit....ah...detailed in training...