There are some good competent instructors in all the agencies, often as not they are handcuffed by juvenile texts that they are forced to use, overly stiff standards that are at the same time too low and too restrictive and agencies who, at base level, do not respect them.
Jim impresses me as a good competent instructor who has escaped from that trap. BoulderJohn and Peter appear to me to be PADI instructors who know how to think outside the PADI box and find creative ways to maneuver through the restrictive PADI thicket. Bob (Greateful Diver) seems to know how to deliver a quality NAUI course (but then NAUI, like SEI, does little to get in the way, making it clear that their affiliated instructors have significant academic freedom).
PADI and SSI are the dominant forces. In my opinion their materials are the worst available and their average instructors the least capable.
Now let's look at your three scenarios:
1.) PADI - OW, AOW, Rescue? - Likely the weakest of the three, three programs with little opportunity for deviation, the best you'll wind up with here is the sum of the three courses, less a bit for repetition and things that are lost (with the exception of a few rare instructors) like teaching neutral, sufficient gas planning, etc. The format of the courses does not lend itself to a holistic approach that integrates the skills in a smooth flow and thus makes the courses multiplicative or better.
2.) NAUI - OW, Rescue, Master Scuba Diver? - This, by definition, should be the best sequence. A NAUI Master Diver is supposed to posses all the water skills and diving knowledge that is expected of a NAUI Instructor ... all that should be missing are the group control, teaching theory, business of diving, legal aspects and NAUI procedures sections. However ... from what I have seen a lot of older NAUI CDs are starting to burn out and many of the new ones are not as good. NAUI granting permission for very small ITCs with minimal staff has significantly eroded the quality of such programs and the QC that used to be part and parcel of having a staff of ten to twenty who were always looking over the CD's shoulder.
3.) Anybody OW, AOW & Rescue + pass GUE Fundamentals at the recreational level? - This is likely the most capable diver that you'll find given the three options, but that is because not all NAUI Instuctors are, from what I have seen and heard, living up to what a NAUI Master Diver should be. Fundies, in this case is both a course and a hurdle, divers getting over that hurdle, even with a recreational pass, must demonstrate rather clear competence. I see slight problems here with over dependence on equipment and "cave blindness" as it relates to the things like snorkel use and free diving skills.
As far as, 'It's the instructor, not the agency,' is concerned: This would be true were we comparing apples and oranges, but we are not. With some rather minor exceptions you can run a NAUI course using PADI materials and schedules ... but the converse is not true. It is possible for a NAUI course to be nothing more than a PADI course at its worst ... with a little rescue thrown in. At the other extreme, however, a NAUI course, run by an instructor who understands how to effectively use the academic freedom permitted by NAUI to custom tune his program to the students' needs will be hard to beat. This level of variance will not exist within PADI, the strictures do not permit it. So it is not just the agency, nor is it just the instructor, but rather ... the major differences lie in the large interactive term of the agency and the instructor ... to attempt to tease them apart is to loose the power of the combination amidst foolish reductionist noise.
I'm looking forward to hearing Thal's answer on this one as well. My 2 cents: As you said, it really is the instructor - not the agency. That said, certain agencies make going above and beyond the minimum standards rather difficult. I'm not aware of any ubiquitously available programs that would meet my criteria for answering that question, taking instructor choice out of the equation. The closest would probably be something like the GUE and UTD open water programs, only because their standards for gaining an instructor rating are relatively quite high (making instructor choice a bit less of an issue), and their published standards for what constitutes mastery at a given level are comprehensive. Thal would probably say that there are still large gaps in those programs when compared to his 100 hour program, and I have no doubt that he's correct about that. I'd still say they probably constitute a more CONSISTENTLY high quality choice when compared to most other recreational diving agencies.
I hope that my answer entertains. I have a lot of respect for the GUE and UTD open water programs, and some differences.
They do an excellent job in about six-tenths the time of a 100 hr course (note: that is not MY course, nor is it Thal's course, it is a course that has been run, with minor changes to accommodate advances in equipment since 1952. It is Jim Stewart's course and Lloyd Austin's course and Glen Egstrom's course and Lee Somer's course. I am but on in a long chain that came before me and continues on after me).
They have defined their target well, preparing a new team member to take a position as a junior team member in a team. Team, team, team ... that's the key to their success and to the effectiveness of what they do. My problems with their approach have less to do with training and its effectiveness and more to do with underlying philosophy. I favor building scuba skills, rather anticlimactically, on top of well tuned free diving skills while UTD and GUE believe that they can create an standardized and equipment dependent situation that will permit a diver to never run out of gas nor be in danger of choking on inhaled water. While I will grant the former, especially in a team format, the latter gives me pause.