I have been bummed about the entire Civ system of whales and fish from the very beginning. I believe that cities should have to produce fishing fleets (similar to colonies) and send them out to where the fish are. Historically, the Dutch, US, Canada and Great Britain have had lots of arguments about fishing rights in George's Bank. This should occur in civ. All that needs to be done is to have fish (and possibly whales) show up in various parts of the seas and oceans (lakes should be done the way they are now, and some fish could still be within a city's radius and therefore exclusive to that civ) and make the various players send out a special colony unit called 'Fishing Fleet'. The fishing fleet could even be attacked (either by pirates or hostile opponents) but would only lose its catch for like 10 turns. This would simulate the fact that the fishermen still know that the fish are there and would return once they rebuilt their own boats. This could even be a negotiable item, i.e. I will give you this tech for all fishing rights at x,y.