These are few things I can think of, I'm sure others can add

-big boards are better in heavier waves, no ski overs you get with little boards
-you can run twice as many lines per side with big boards
-like said, you fight the fish the whole time with big boards
-little trash fish are easier to see and clear the line to rebait on big boards
-you can run any kind of lure with any kind of weight or diver on big board
-running big boards with a good bungee system stabilizes the boat in heavier weather
-it takes less time to teach new people how to run the big board system
-trying to run lightly pulling lures in gusting winds is more difficult with big boards as they tend to want to wrap the fishing line around the tow line
-little boards are quicker to deploy and pick up

I'll add that the Skipper9 system of running big boards, in my opinion, is unbeatable for running a lot of people and catching a lot of fish quickly. You bring the fish to the boat when you're ready for them and as fast as the crew can work.

Greg