This thread, like every one that involves PADI, will probably explode into several pages, with all the regular contributors...
Simply put: it doesn't really matter.
I've got certifications from PADI, NAUI, SDI, NSS-CDS and NACD. Never had a problem with any of them being accepted.
Why can I be certain it doesn't matter? Because many instructors can teach for several agencies. Same instructor...the only difference in the class is the book. There are only a limited number of skills that different agencies want taught in some special manner, and for the most part, the class is taught almost the same no matter what agency the student wants a certification from.
PADI's books include more self quizzes and things, which many people find helpful. NAUI's materials assume you know how to study.
You can go with one now, and switch in future classes: OW can be PADI, AOW can be Naui, Rescue can be SDI, Divemaster can be SSI...it doesn't really matter.
Still, this thread will soon be rife with people arguing that this or that or the other agency sucks. The largest difference, by far, will be the instructor. See if you can find out information on various dive shops in your area on Scubaboard (go to your regional forum, or use the search function with various dive center names, just be careful there, because there are lots of shops with the same name around the globe). Take what you read with a grain of salt, but if a lot of people say the same thing, it might be true.
Good luck and dive safe!