I think a good resolution for the size issue is to have two different classes of warships.
One class would contain ships that are about the size they already are, charachterized by being light, small, fast ships that could easily pass through a 3-tile stream and would generally be armed with a few arrows (shot from deck) and transports with room for about 5 units.
The other class would consist of capital ships and heavy transports, with the big mounted siege weapons, realistic size, slower movement, and lots af archer power. Unable to enter any waterway less than 5 tiles large, they would have to stick to the sea. The tranports would hold 10+ units, and mabye the warships could carry a few. (warships were used as transports until the 1600s)
Of course, the big ships would be able to crush the smaller boats, while the small ships could outrace any larger vessel. Just a thought.