Yes, yes, yes. Give me fleets & ships, and much much more. With ships installed, many things become possible...
1] Like Civ, you can determine how much water you want your random world to generate.
2] You can have more interesting quests (something like Sinbad had).
3] You can have ship-to-ship battles.
4] You can plot (or defend) overseas invasions
5] You can have fantasy water monsters.
6] You might be able to discover (or create) underwater cities.
7] With water/oceans in the game, people may be inclined to play on larger maps.
8] It would be fun to be able to design/build different kinds (and sizes) of ships, with many different purposes/abilities, and
9] You could have wonderful 'tactical' combat fighting on the decks of ships
With the GalCiv development team up to their waists in problem issues to fix/finish in FE, I'm sure they would welcome the challenge of adding on a major new component to the game. 
On the other hand, who better to design ship concepts then the development team that designed all the space ship elements in Galactic Civilizations?
On the practical side, I must concede that this kind of expansion for Fallen Enchantress is probably best left for a future expansion pack. The development team has many more important issues on their plate at the moment just fixing and finishing the development for the basic game so that it can have its official release. After that, perhaps, who knows? Keeping my fingers crossed.
