Random ideas I've had while playing Windrose:
Expeditions: these would allow captains to travel to different parts of the world, each with their own unique biomes, quests, resources, and systems. Rather than trying to cram several biomes into a single worldspace with little logic behind their placement, Expeditions would provide multiple themed worldspaces.
Arctic: Hunt whales with new harpoon cannons across frigid seas. Explore Taiga and Glacier biomes to hunt polar bears and seals. Collect blubber to keep your camps fueled and ships warm. Trade with the Inuit and help them deal with a supernatural threat (keeping in theme with the current storyline). Fight the British Empire and stop them from uncovering the Northwest Passage.
Mediterranean: Fight the Barbary Pirates across North Africa's coast. Defend Malta and its nearby islands from raids, and free those captured from Barbary camps. Hunt (ride?) camels across desert and arid rocky islands. Wheel and deal with representatives from other empires to suppress the pirate threat.
Riau Archipelago: Help the Sultan of Johor wrest control of the region from the Portuguese Empire, and build the city that would eventually become the legendary Singapore. Smuggle spices and exotic goods between patrols, and defend yourself from vicious macaques and tigers in dense rainforests and jungles.
Black Sea: A more temperate region, but rife with competition between the Russian and Ottoman Empires. Play both sides against each other to enrich yourself. Start your own fleet of privateers to support or attack either or both Empires, and build a capital to put both Moscow and Istanbul to shame.