Awesome mod Kael! I don't pay vanilla anymore. I just wanted to add in my own feedback.
First, the penalty for not using Free Trade if you are using the civic unlocked by your state religion should be reduced. I shouldn't be getting +8

in each of my cities if I'm playing fellowship of leaves and I have the Guardian of Nature civic. That's a huge penalty that ultimately forced me to switch civics even though I was keeping my lands heavily wooded.
Second, the range on the birds carried by some units needs to be upped just a tad. It's quickly obsoleted by the vision promotion.
Someone else in the thread mentioned traps. I think with the fast speed of the units, something needs to be done to slow down units crossing into your lands, and this could help.
Another idea would be the ability to construct walls in tiles that would stop movement until destroyed. Building a wall in a narrow passage could buy you a bit of time to prepare against an aggressive enemy who keeps sending his units behind your front lines and harrassing workers and improvements.
As for 5 different types of unique ships, here are my suggestions based upon religion.
Fellowship of Leaves: Fast ships that have higher withdrawal rates, but less attack power.
Maybe allow them to carry a scout bird (with longer range) onboard like the ranger/druid/beastmaster line.
Runes of Killmorph: Slow ships with high armor and attack power.
Maybe allow them to bombard.
Ashen Veil: Ghost ships. Cannot be seen in the open ocean.
Maybe add the ability to spread a disease.
Octopus Overlords: Giant squid (obviously

). Have the ability to heal themselves by attacking other ships. (feeding off of the sailors) Maybe let them submerge to heal; while submerged, cannot be seen or attacked. This one wouldn't be fully possible though without the SDK. ( though you could give a ship unit these properties until then and we can pretend it looks like a squid.

)
The Order: Medic ships that have the medic promotion. This one is stumping me a bit. I only have one idea for them, and it's maybe a little imbalanced: let them fly through the air.