Enjoyed your report; very even-handed, the good and the bad. Sounds like a good trip overall. A few thoughts:
1.) Some destinations with simple travel arrangements I book myself; some with more complex arrangements I'd be inclined to use a travel agent. The aggravations and change-ups you encountered make this sound like one of the latter.
2.) I was reading your report earlier on my iPhone 7Plus at a restaurant; the text was tiny. It doesn't reformat so if I zoom a bit for readability, it's wider than my screen. Maybe not many people read your reports this way, but maybe of interest.
3.) So the Mexican camera tax rip-off appears to be an ongoing thing? Good to know.
4.) You identified the logistics issues; a 6 day trip spread over parts of 2 weeks (not a good match for working people taking time off; why do they do it that way?), and a bit of 'stop and go' travel hassles (which isn't what live-aboard trips are generally about).
5.) Since the pelagics are seasonal, what time of year would you want to go on a return trip?
6.) Roughly what did this trip cost the divers for the live-aboard, and if you counted other related expenses (e.g.: a night at a hotel if needed, transportation), roughly what cost without airfare would this? How many dives (and how many of those in Cabo Pulmo) for that?
I ask because some people may weigh this trip option against others in the region, perhaps as a once in a lifetime thing. So, for example, they might consider it against a live-aboard trip to the Socorros. Just trying to get a since of the ins and outs.
Thanks for sharing your detailed experience!