When people say ships they always think of mobile Garrisons/Order Halls which would be very vague if you ask me. Sure, having a crew and sending them to missions would be great but why not have a goal like... being the King of the Great Sea?
If they let us traverse the Great Sea then there should be randomly generated islands with random loot, monsters, a mini non-instanced dungeon and obstacles. Not big islands like Kezan or Zandalar or Kul Tiras but smaller, unknown ones. Those that don't appear on the map. We should be able to claim those islands as our own and place our banners there. Fight with other factions' ships or pirate crews. Things like that.
But that might be extremely hard to implement because we know how outdated the engine is.