Historically, naval battles were a combination of ramming and boarding, with very limited role of on-board archers I believe ?
Also a few catapults on Roman ships, and incendiary traits sometime used by some, and of course greek fire.
But to have interesting tactics using such technologies, I guess that the game would need a different scale as it had been pointed out ?
About the anti-infantry use of ships (that is overpowered as of now) :
If the ships are made less efficient against infantry/buildings and cannot anymore by themselves interdict a land strait, they would need a specific togglable mode for their onboard infantry "disembark, destroy and re-embark" so that they could be put near a land strait (like Gibraltar in the Meditteranean map, where as of now putting two warships allow to kill all merchant convoys between north and south) and have the onboard infantry destroy any enemy coming near (unless of course the enemy is strong enough to defeat said infantry).
Also, ships would need a slow healing effect, so that it's possible to use such tactics without micro-healing the troops.