I suggest adding a new mode for Arena called "Fleet Clash." In this mode you'll have two teams of ships go head to head in a competition to secure a control zone that will periodically move positions. Points will also be earned for kills of either whole ships or individual pirates.
Teams will consist of all three ship types, one type for each team. The crews will have the ability to either queue for the ship of their choice, or be fitted into whichever ship needs more crew. Crews without enough deck hands will have the option of opening their ship to other pirates for mid game joining.