Don, other than GUE which is very different, it was my understanding there was no significant difference among the others. I'd appreciate hearing from you what the differences are -- thanks. (And yes, I know some have "apprentice" but it sounds like you think it is more than that.)
While the course progression and limits for NACD, NSS-CDS, IANTD, and TDI are similar, there are difference for courses with NAUI, GUE, and UTD.
In addition, there's difference in methodologies. Some agencies are strict or rigorous (depending on your perspective) and others offer their instructors flexibility or slop (depending on your perspective). As the result, there are classes that are more like mentorships, some classes that heavily focus on individual skills, and some classes that heavily focus on team skills. With regards to drills, some classes have individual failures, other classes compound failures, and other classes have what some may say have an unrealistic number of failures (of course, those who have taken these courses will offer that the number of failures is not the point).
With regards to standards, some agencies are strict/rigorous and others allow their instructors to make the determination of student success. For example, while every agency mentions "trim" or "buoyancy" in their standards, how theses standards are interpreted are different among agencies and their instructors. For cave specific drills, what about the lost line drill? Is finding the line a success criteria?
At the end of day, the course you choose will affect the way you dive and look at the cave. However, I'm not going to say which one is the best for every diver. Each person has to make a decision for themselves.