I am a PADI instructor, was an IANTD instructor and have certifications from TDI, CDAA,SSI and others.
First of all what the others have written about instructors is correct I have see good ones and bad ones regardless of the agency.
There is always an issue of certifying agency pride especially with the smaller more technical agencies. CDAA divers for example consider their teaching standards to be higher than others. BSAC graduates are similar
As a past teaching professionsl I rate PADI's instructional materials typically superior to the others in terms of presentation, structure, neatness etc.
Some of the course materials I have had were very basic and in some cases quite poor in terms of presentation and the coverage of the material. If you are learning from a non-PADI institution you often have to rely on the knowledge of the Instructor to get all of the theory out. With the PADI materials it is all there.
The PADI teaching methodology is exactly that a methodology and it is designed that way to keep some consistancy between instructors all over the world. It is also designed to protect their instructors in case of a problem, i.e. if you follow all the steps and cover all the requirements then it is usually the methodology that goes on trial not the instructor.
Bottom line however is your instructor if they know what they are doing, want to teach you and cover the required skill then it doesn't matter what agency (I mean the major ones here) you use.