Current boat fighting i think can be improved a lot. Right now it works same as siege tower in water. 2 features which I think are feasible can be added.
Option 1:
Visible garrsion: It should be visible how many units are there on boat: Some one has already developed this mod of visible garrsion.
Attackable units: Units should be attackable. This is work same as walls. The unit can attack other in unit in their range that means boats with archers will have higher range compared
One of the things I find frustrating with naval maps is that you have to meticulously garrison your soldiers onto different boats. It would be nice if there was a button that functioned kind of like the town bell, but triggered from the boats.
Select a boat or boats
Press a "board boats" button in the gui panel.
Nearby military units evenly distribute themselves onto the boats.