I dove with AKR through a cruise ship last week and what the posters said above is true. There was zero worry about timing, but then again, the dive was all about efficiency. AKR is very professional and everything ran smoothly, but the dives were 40 and 45 minutes and I finished both dives with 1200 PSI in the tank and was back at the ship with 2.5 hours to spare -- not quite enough to go to a West End beach, but just enough to wish some of that extra time had been spent under water diving. The dives themselves were pleasurable and even though there were 15 other divers on my boat, everything went so smoothly you could hardly tell. people got in and out of gear and in and out of the water pretty efficiently. Good briefing and good leadership from the DM's. The only downside was limited (in my opinion) bottom time. In Cozumel on the same cruise I booked separately with Aldora and got 60 and 73 minute drift dives with just 5 divers on the boat.
If you want personalized attention or longer bottom times, go separately. But if you're flexible and don't want to think about it, go with the cruise ship's excursion, at least in a place like Roatan where they contract with a good dive op.
THe upside of the ship's operator, not mentioned above, is the social angle. You get to meet more of your fellow cruise passengers, which can be a plus. My wife doesn't dive so I didn't bring my own buddy and met folks on the way there. I met people on my non-cruise-arranged dive too, but I knew I wouldn't be seeing them again.
