The Merchant Ships have a superfluous Bombard ability.
Also, do we have a specific discussion I've missed regarding the ships' tech tree?
Eclipse had sent me an excel sheet with all the ship units a while ago. In fact, I would already have attached it here, but I noticed that it is not up-to-date. I assume it represents some kind of "original state" of the ship unit tree in the original scenario before TheGuardian (or was it Againsttheflow?!) did his modifications of the ship tree. So the excel is of little value to us and would probably confuse more than help.
But in order to simplify the ships a bit, I can imagine a setup like the following. Basically there would be 5 classes of ships:
Heavy Warship |Slower but heavily armed warship|Can transport "light troops" (e.g. musketmen and the like). Lethal bombard.
Merchant Ship |No combat value, used only for transportation|Can transport "treasure units" and workers/settlers
Troop Transport |No combat value, used only for transportation|Can transport "heavy troops" (Marines, Line Infantry, Cavalry, Artillery)
Pirate Ship |Fast and medium armed warship|Can transport everything. Hidden nationality. Pirate tribes can build it from the beginning, other nations need to research "Letter of Marque" first.
The first two classes would be available in two "flavors": one for the English/French/Netherlands ("Frigate", "Ship of the Line") and one for the Spanish/Portuguese ("Galleon", "Royal Galleon").
Also the Pirate Ships would be available in two "flavors": one for the Pirate tribes (requires the "Pirate" resource) and one for the remaining nations (does not require a resource, but requires "Letter of Marque"). The "Pirate" flavor should be faster, stronger and cheaper than the "European" flavor.
Also, each ship class has a three-level upgrade path, where each new ship generation has some distinct advantages over the predecessor version in terms of faster movement and/or increased hitpoints and/or increased A/D/B values and/or increased transport capacity and/or additional special abilities (lethal bombardment, blitz, enslavement).
This would give us a total of 24 different ships in the game (but only 15 of them buildable by one given nation), instead of the zoo of 60-70 buildable ships we currently have... In addition we could think about having one more ship as unique unit for each nation, which can trigger the Golden Age.
How does that sound?
There is one problem though: I have only very basic modding knowledge and I'm not sure, whether I'll be able to implement this system. Especially I would have to figure out, how "treasure" units can be loaded into a ship directly without first being "picked up" by a foot unit. However, we all know that this is possible, because El Justo did exactly that in his AoI scenario. (So I guess, we'll need to ask him for a tip or two...)