I’d also add small boats being able to cross shallows to the list. It would make maps more accessible to fishing boats.
Melee naval combat is a must, and could be part of the basis of a counter system that isn’t just bigger boats and buildings win.
Maybe instead of naval population, there could be an upgrade where you get to choose to increase the build limit of only one kind of ship. So you could have options of +1 Frigate, +2 Galeons, or +3 Caravels, etc. That would allow you to have a bit more diversity in unit compositions.