Several times a year I get asked if I should stay with -blank- certification agency or is -blank- better. I am sure that some people feel very passionate about their certification agencies and I have to say that I like the onces I have dealt with. These include PADI, NAUI, SSI, TDI, NACD, etc.
In my opinion, there is no single better agency for general scuba training then another. Even when you get the more advanced skills many of the agencies teach a lot, if not all, of the same concepts. It really all boils down to the instructor teaching the class. If you like your instructor, you are probably going to have a good class. If you don't like your instructor, you probably are not going to continue further into the sport.
That being said, there are always exceptions.