Saltair:It is more important to get a good instructor that you are comfortable with than the certification agency. I am NAUI my wife is working on PADI I am planning PADI AOW in the spring. They are interchangable. Quality of instruction is the key. Being brand new you may not be in a position to judge who is best so ask around.
As you can probably tell, not all of us agree that the agency isn't important. While a good instructor with a bad agency CAN teach a good class, any instructor with a good agency WILL teach a good class because the agency DEMANDS it!
Let me say this one more time. A good agency demands that the instructor teach a good class. If "good" isn't built into the training standards of the agency you have NO reason to expect it.
You are right. The quality of instruction is key but the place to start is with an agency that teaches their instructors how to provide quality instruction and insistes that they do.
Sorry to rant but we hear this all the time, that the instructor is more important than the agency. However, that's only true because the mainstream agencies aren't any good and they permit their instructors to teach lousy classes...which of course meet agency requirements. You have to find an instructor that has learned how and decided to teach good classes on his/her own with the agency being no help.