That's a good idea. Also the ideas of reefs and such would make things more interesting.
One other thing that might be nice is to have low tech ships need to stay close to the shore. Ships did not venture into the open seas initially in real life afterall. It would be a way to have naval technology matter more than just always getting stronger or faster ships. It just would require a new sea tile.
I do agree sea tiles could be lived up. Heck, before agriculture fishing and local water life was the major factor for cities and towns. Not just for food, but commerce. WHERE ARE THE RIVER TILES??? (giving you a hard time, Forggie, but it is getting late in the game). Right now I feel there should be an option for how much water there is in the world. Sea faring means little and it was a rather large factor in history.
Some monsters wouldn't suck, storm fronts would for sea as well as land.
The sea has been pretty lame thus far. Hopefully it will get attention soon.
[edit] I really like the reef idea