No pirate ever had just one ship. No, they had many!
Imagine Fleets being SoT's Clan system where you and your friends can fly under the same flag. Your emblem would appear as the middle mast flag like the shark hunters, jolly roger, etc.
The real purpose is so you can have 2-3 ships sail as a fleet to conquer the oceans and flank forts or enemy ships to get the upper hand. It's add for me fun and more challenge as you avoid a British Imperial Navy type faction with your chests of loot. Imagine the open sea battles as one fleet takes on the next over control of Thieves' Haven and the treasure stashed there. Players could even make alliances with them for protection.
Also, why not allow ships to be named? Everyone has a name they'd call their ship. So why not allow non-offensive names to be implemented and shown on the sign above the captains quarters? It's already there, just let us throw a name up there
