I have a couple of suggestions for the subdued animals. Not being much of a modder at all, I have no idea how difficult these would be to implement.
First, this has already been suggested, but it there any chance of getting more thematic promotions for aquatic animals? That woodsman promotion sure looks funny on my subdued minkie whale, but at least that promotion gives some benefit to the whale. There are other available promotions that are totally useless to aquatic animals.
Second, why not allow some subdued aquatic animals, like whales and sharks, enter ocean squares. Since they can't explore and they can't transport troops, I don't see why this shouldn't be allowed. It seems strange when a shark can't cross one or two squares of discovered ocean to get to another already discovered coastal square (instead of having to hug the coast).
Third, I have an idea for flying birds. Why not let them fly over water so long as they end their turn on a land tile.