1.) More men - good for city attacks
2.) More room for goods and supplies - sell them all in a wealthy town
3.) Having both a fully upgraded Royal Sloop and a Large Frigate is a good idea
4.) Treasure Galleons make great mules (140 cargo)
5.) as Quentin said
6.) if you have not enough men to man your main ship, you might want to sink captured ships: You will need a minimum crew on every ship, so you should take this in account if you have few men.