Remember how the ferry in FFXI would be boarded by skeletons summoned by pirate necromancers? Limsa's story talks a lot about pirates and sea battles, but there is minimal naval content. The most we get is a boring ferry (and I don't use the word "boring" loosely when I talk about FF) and a few cutscenes. I want to help fishing boats fend off monsters, or defend freight ships from pirates! It doesn't even have to be that complicated to program, although I suppose they could include a cannon firing feature. I just want to see more of the sea so I can feel more like a member of the Maelstrom fleet.
Of course, to balance things out the other two cities would need unique battle types as well.