The difference is the time you eat.
Sorry, I had to. First seating is normally full and has more children. People don't want to eat so late with their young children. Second seating is less full, which can mean both better service and a higher chance of getting a table request. I've never seen or heard of the main restaurants running out of a dish during second seating, so I don't think it's something to consider.
Another thing to consider is your port schedule. If you'll be in port late, you may want a later dining time to accommodate excursions.