So there really is no point of making boats, mayby except for the bombard ship (wich is way to costly at resources and command points) because they take way too much CP in general and there is really no point of dominating the sea.
So why not make some changes to the existing ships and mayby make a new one?
-TRANSPORT SHIP
Let transport ship have the ability to gain resources!
It will be a transport ship like usual when it comes out after being purchased from the dock, but it can gain resources when it is deployed (deployed like the dwarven ram ability)
It should not have the ability to deploy when it transports units then the icon for deployment should be greyed out.
Resources gained should be 10 resources every 10 seconds (or more resources, if it is needed)
It should also get upgrades like other resource buildings (farm, mine, e.t.c) but it will lose the upgrade when it is undeployed.
-BOATS IN GENERAL
All good side boats should get rid of the passive heal upgrade and give it damage upgrade instead.
Boats being near owned or allied docks should get passive healing.
-A NEW "HERO" SHIP
Every faction should get a unique special ship you can only have 1 of.
This ship is larger then battleships (may have the same model?) but it has several passive and active abilitys that fits naval warfare.