Well, with the big boats for, say, 20 divers the pros are that you'll have a platform that makes it easy to get in and out of the water. And a bathroom on board and sometimes room for sunbathing on the way out to the site and back.
On the downside, with a larger group of divers, you're much more likely to have a mix of experience levels. That means that if, say, 1 diver runs low on air before everyone else, usually the DM will make everybody come up -whether they're low on air or not. This will generally be the scenario unless it's a place like Dive House, one of the ops I used to work with before I became an independent instructor. Dive House takes along a second DM for mixed groups.
The small boats --carrying 6 to 8 divers max -- don't have the bathrooms - although you should be sure to choose one that has a sun shade and a ladder. And they don't have a platform. But you get a whole lot more personalized service -- which is why I always recommend this option as the first choice if you don't have special needs that require the big boats . In addition to getting a lot more special attention, the small boats allow for considerably more multi-level diving than is possible with a large group. And the small boats are faster so they can usually get you out to the reefs ahead of any crowds.