It's all about insurance. Sure you can find operators on shore but you are taking a risk. I don't mean that the independent dive operators don't care if you get back to the ship or not. I mean that sometimes unforeseen things happen and you are late to the dock. Maybe there are engine problems with the dive boat or who knows what. The extra money you pay for the ship-arranged excursion means you will not be left, no matter what. If the boat breaks down in the middle of the ocean, the cruise ship will be notified and will wait until you get back or are picked up.
This also means quality insurance. If the boat advertises a beautiful coral reef and all you get is a patch of reef, many times the cruise ship will refund a portion or all of your money. Of course that depends on circumstances. If it's out of the operator's control then there's no refund but if the operator takes you to a crap area to dive in order to save on fuel then it is researched and usually at least a portion of the money is returned by the end of cruise. It also means that the operator has been researched and checked out by the cruise staff. The shore excursion staff goes on these tours all the time to make sure they are running as they are advertised. Many cruise lines have dive instructors on-staff that go on these tours "undercover" for quality assurance purposes. I know because I've done it. I've seen a private operator that had an inflator hose completely severed with a cork in the end. I've seen deep dives run with no depth gauge provided to the guests. I've seen BCDs with holes in the bladder. All of these things are monitored by the ship-arranged tours.
I don't agree that you get a cattle boat of divers. Sure you get a lot of mixed experience but that isn't specific to cruise ship tours, that's any dive operator in a tourist destination. "Cattle boat" is something I would reserve for snorkeling trips but not diving trips. I have seen snorkeling trips with over 100 people on one boat before. I've never seen a dive operator arranged by the cruise ship with more than 12 people on board.
Do what you want but I would save the self-arranged tours for somewhere other than Belize. In Belize you usually have a 15-20 minute wait just to get on or off a tender going to or from shore. Then you have a 10-15 minute ride to the shore or ship. That takes up a lot of time and makes it even more difficult to arrange your own tour in the short amount of time you have. If you arrange a dive through the ship then you typically get off the ship an hour before anyone else can expect to touch shore. Even the other excursions like Mayan ruins are best arranged through the cruise ship. To get to Xunantunich is a 2-2.5 hour ride into the jungle. We've had people left in the jungle or a van break down in the jungle and have to fly themselves to the next port. Belize is NOT the place to be arranging your own tours and it certainly leaves much to be desired as far as shopping goes.
Take this from someone who has been to Belize over forty times and has seen people left behind while the others are sipping margaritas in the bar watching Belize disappear behind us.
