Finally got around to playing a game (as Calabim) with your mod. Naval AI seems much improved (from it's previously non-existent state, anyway), but I have some issues:
1. Galleys are too powerful for the early game. I like the ability to enter ocean with optics, but I'd put movement and cargo both at 2 (down from 3 and 4, respectively). Enough to send a settler and escort to another continent, but not allow for huge amphibious landings so early.
2. Caravels, being out of the upgrade trees, are next to worthless now, yet the AI wastes time and resources building them, even after they can build better ships. Not sure what to suggest as a better solution.
3. Galleons upgrading to Queen of the Line is a mistake, IMO. Queens are, to my play method, inferior ships. The +2 combat (7-->9) and +2 cargo (8-->10) pale in comparison to their -2 speed (5-->3). Transports have no business in combat anyway, and once you are able to build Queens, you can't build Galleons at all.
4. Cargo capacities seem high across the board for the transport line. I'd recommend:
Galley: 2 --> Caravel: 3 --> Galleon: 4
Queen of the Line: 6 or 8 (fresh build, not an upgrade, or increase speed to match Galleon)
Trireme --> Frigate --> Man 'O War
5. Not sure if they're intended or not, but I'm seeing some unusual barbarian units, including freaks, various religious disciples, lightbringers, and lunatics randomly wandering around.