I've been playing with the editor and am testing the changes I've made to the unit strengths and abilities, for all units, not just naval units.
Some of the more interesting changes are to the bombardment values and unit abilities. Starting with Galleys, I've decreased their speed to two and made them strictly coastal vessels. Their attack and defense are set to 2. This corresponds to the main weapons they would have used: rams, arrows and swords. And they can only carry foot units. No room on a galley for horses. Caravels are given a similar attack and defense, but move faster at 4, and can carry 2 units, includng mounted. They can only travel in Seas. Galleons get strengths improved to 4, move a little faster at 6, and can carry 3 units. They have a limited bombardment at strength 4, range 1, RoF 1. Privateers are similar, but don't carry any units. Frigates become a little more powerful with strengths at 8, can carry 1 unit (proto marines?) bombardment at 8/1/1.
When you get to modern units like Ironclads, you have a major leap in technology, since you aren't limited by sails and wooden construction. Bear in mind to, that these settings are abstractions of groups of vessels, not individual ships.
The increased bombardment values match the changes of land based units, and the changes to the special abilities get nastier. What should happen is that a modern unit should be able to destroy an older unit without taking massive amounts of damage. A (Spanish) Galleon should grind a (Greek) trireme under if they crossed paths. Mass and small cannons beat oars and rams
I will try to post a spread sheet I've been using to track the changes I've been making so you can make your own changes to taste.