Any time you're dealing with water, you're dealing with trade. Water travel is the fastest, easiest method to ship large amounts of stuff around. That means you can come up with everything from political intrigue to exploration to empire building to (counter-)piracy.
You can also make your own version of the Odyssey; your players are on a ship, blown way off course, and have to find their way home.
Also, a low-tech FTL is also fun; your characters have vital information to the defense of their homeland and must reach home before they're chased down by the enemy armada.
