It's all in your mind. There are no agency wars. The agencies get along with each other and cooperate by recognizing each other's certifications. When I go diving, I ask my buddy about his experience and comfort level, but I don't ask him through which agency he's been certified.
What does happen is a potential diver or a new diver will discover that there is more than one agency. Usually they will know about PADI and learn about NAUI (or vice versa, but not as often), but sometimes it will be another agency. Since PADI is so big, it's almost always one of the two. That person will be curious and will ask about differences between the two agencies. Misinformed people will answer that there is no difference while others will explain the very real differences. The discussion often goes downhill pretty quickly into the "no difference" crowd calling those who point out differences elitists and compare the non-PADI approach to SEAL training (both of which are silly) and those who point out differences saying something stupid like PADI = Put Another Dollar In. There are those on both sides who do not engage in such childish behavior, but it's found in most of the threads. That childish behavior makes it look like there are agency wars when, in fact, none exist.