Hi, I did go to Ogasawara again this year. The weather was a bit of a problem, we couldn't get to the farthest dive sites.... but we still saw whales on many boat rides, and heard them underwater on some dives.
Diving is controlled by the boat crew, with strong currents and only one boat I understand why they don't let you buddy dive outside the guided group - it would be a recipe for disaster chasing buddy pairs across large areas of ocean in heavy swell.
Most dives were 40-60 minutes, depending on depth, air consumption and nitrogen loading.
I would go again in a heartbeat.
By the way, I have not experienced much of this "40-minute nonsense" but I don't dive with Japanese diveshops so much - most places I have been to will let you shore dive without a shop guide at your discretion - especially if you have a divemaster/instructor in your group.
Lots of places cater to the lowest common denominator, and that is as true for shop guided dives in Japan as it is anywhere else in the world. The vast majority of my (admittedly only 300 or so) dives in Japan have been free of any 40 minute restriction.