I'd Like to see a Sky Fortress as the "FC Airship". Within it, you can dock the member's ships.

FC members maintain the Sky Fortress. Maybe give it a durability system like gear that requires multiple people to maintain it. New items that function as Dark Matter. Each item only recovers a certain % of durability, so you'll need lots of these repair mats to fully repair a ship or the fortress.

Player ships can have NPC crew members they can hire. Maybe have these NPCs paid with Ventures. They can be assigned to a specific system. Manned systems are much more efficient:

Navigator - Adds PoIs to the minimap (enemies, friends, objectives, etc.)
Pilot - You
Weapons Specialist - Improves Weapon attack/reload/accuracy
Engineer - Repairs HP in battle (sorta like giving your ship Regen)
Comms - allows you to talk with other ships (maybe like a party made of ships instead of people).

3 different sizes like housing. Have an airship level. As the airship levels up, more equipment like advanced weaponry or reinforced hulls become equip able. This is so people can't "twink" their ships and gives a market for those low level hulls and weapons.

Story could be that Eorzea decides to counterattack Garlemald while they are still recovering from the failed invasion. Players use their ships to blow a hole in their front lines and to take the Empire's attention from the guys on the ground. OOOOOOO, I could talk about this for hours!