All my certification thus far has been through NAUI. I chose NAUI because it's a non-profit. The primary responsibility of a for-profit entity is not the consumer, but rather to the owners/shareholders. This is not a bad thing, but it is the way the structure works. Many would argue that a for-profit entity has to provide a better level of service in order to remain competitive. However, I wanted my training done by an agency that did not have a primary responsibility to someone other than me.
That said, I have had three different instructors for my four NAUI certifications (OW, AOW, Nitrox, Cavern), and while I liked them all, there was a lot of variability in the quality, and the different instructors even, to some extent, challenged the quality of the others.
I am not wedded to NAUI; my next courses may not be through NAUI (rescue, advanced Nitrox & deco, cave). I'm looking first at NAUI shops for Rescue, but if I can't find a course that fits my schedule through one, I'll go to another agency. And for the more technical training, I'm leaning towards an agency that specialized in that aspect of training (cave: NACD or NSS-CDS, both non-profits).