Will,
I've done three cruises in the last year, and I leave next week on my fourth. All of these have been "diving" cruises, where I use the ship for room and board, and that's about it.
One big thing about excursions is that they are usually geared towards newer divers. They have to set themselves up for the lowest common denominator, because they have to take everyone that comes along. Local dive shops can turn away people who don't make them feel comfortable, where an excursion is a done deal.
Cruise excursions usually run about 10-40% over what you could book yourself. However, they have some advantages that have already been addressed - number one of which the boat won't leave without you. Another advantage is if the times the ship is in port makes it hard to book your own, you can still dive.
Some of the negatives people talk a lot about are the additional cost, cattle boat ops, and "cruise ship divers".
Additional cost is there. But if you have to take a taxi to a dive op you've booked yourself, then it's a break-even. If you miss the boat, the excursion would have been much, much, much cheaper. One negative though is that sometimes the cruise ship will cancel your excursion if they don't have enough people going on the trip. That sucks.
The rumor mill is that an excursion will be a boat for fifty divers, and sixty will be on board. Most every time I've used an excursion, there have only been a few other divers on the boat. Occasionally, it's just my wife and I. I wouldn't consider this a negative. On the other hand, you will on occasion be put on a snorkel boat. This is ok, but not really what you want. You end up diving on a shallow (-30') reef that snorkelers can enjoy too. If you are in a small group of divers, it's still enjoyable, but you really don't have the elbow room if there's more than six divers. One other negative about excursions is that often times your bottom time will be shortened, because the operator has to get you back to the boat at a set time. I've never really had the feeling my dive was too short, though sometimes I've come up with more air than I'd have liked.
As far as the "cruise ship diver" mentality, CS divers are traditionally the newbies. The attitude about them is that they are unsafe, borrow all their equipment so they don't know how to use it properly, and have all the other associated new diver issues. Compound that with the idea that they are rude and cheap. Toss all that BS out. Every excursion I've used, the other people have been friendly and outgoing, and it's been a very enjoyable time. There are exceptions, but for me, a good time has been the norm.
Generally speaking, I book my own dive trips with local operators I've found out about from ScubaBoard. If I can't make a comfortable reservation due to availability or times, I'll use the ship's excursion. I have however been diving in several different ports of call, and feel like I've got the cruise ship routine down. If this is your first cruise, I'd use excursions just for the peace of mind. Then, when you are more comfortable with your skills and equipment, and more familiar with where you are going, you can branch out into the local self-arranged scene.
There's my two cents. Keep in mind I'm a very conservative diver, though, and I tend to play it safe, as opposed to more adventuresome.
