May I suggest taking away the generic blue coloring for swamp water, and making it semi-transparent? You would see rippling in the water and such, but it would obscure what is below the surface-though you might see general hazy shapes. This would also allow you to see the riverbed. For that matter, multi z-level rivers would also be interesting. Making the color reflect the current weather conditions on the surface (cloudly, raining, clear sky, snowing etc) would also make it more interesting. This might end up in the init options though. Still, it would make bodies of water far more interesting.
Also, I would like to mention actual ocean tides (high/low), tidal pools (may fill up with trapped fish, other creature, and barnacles growing on rocks below the high tide line as features which would make the oceans in specifc more interesting. Adding in kelp forests and coral reefs for tropical regions-the former of which could contain kelp (cookable but not brewable), sea urchins and otters, and various kinds of fish. Kelp is often visible at the surface, by the way, and grows VERY fast, so this should be represented. This would also provide a good way to train swimming, by assigning dwarves to collect in the shallows, and then assigning them to collect stuff from the kelp forests.
Coral reefs could serve as a source of coral, but more importantly as a way to get crabs, shrimp, and loads of vermin fish. They could also provide places where reef-dwelling sharks can congregate...providing a way for you to obtain that sharksin leather your count wants.
And even more meat. And of course, shark skulls!
Then there are oyster reefs. Exactly like it says on the tin, these are places where oysters are abundant enough to form whole reefs. Along the same lines, mussels may be able to form similair reefs along the shore.
Sunken ships could provide a free artifact or two, and may be able to provide wine or oils, along with metal bars and the like. Coins may also be present in them. Could also serve as a way to get otherwise unobtainable goods.
Edit: kelp forests are generally temperate features, I believe.