It would be more a mod to get around, do you know Achimedes Ships mod? It lets you make a custom airship or boat. They player would be able to grow the airship with things found in dungeons who will be in mountain tops or in the bottom of a ravine.
It is still very much just an idea. I have first to wait until the mod updates to 1.9 and see if I can also make the travelling interesting and dangerous. To mind comes making narrow passages to which the player would need to adjust the ship, and shooting threats so you will need walls and maybe need to protect the ballon? (No idea yet if the ballon can burn or not.)
A huge sky-map with floating islands, dungeons, and stuff. Exploration over 9000!