Hey Dale, great mod! About to complete my second game, now with the Spanish. First was with the Portuguese.
I also have some feedback for you:
I'm with slackerpride and kaiabayashi on this one. When the Indians offer you their settlement, it shouldn't just disappear without you gaining anything. You should get the same benifits you receive when you take an Indian settlement. So, a converted native or two plus some money in the form of a treasure. That's my opinion.
Regarding the pirates, I have numerous issues with them, though I do think they're a nice addition! I'll keep those to myself though as you're still working on them. I'm liking the look of the Tortuga screen though. Looks sweet.

One thing I will say though...is there a way for the pirates to appear later in the game? This would be more realistic and solve the problem that some people have complained about regarding the pirates hogging their ships and basically making some games unplayable.
As it is now, building a navy is pretty much pointless. No matter how many ships you build, you can't contend one bit with the King's navy because their man-o-wars have a strength of 15. I think, if they keep their strength of 15, ships of the line should be raised to at least 12 or 13. Ideally, I'd make it like this:
Caravel: 3
Merchantman: 4
Galleon and Privateer: 6
Frigate: 8
Ship-of-the-Line: 10
Man-O-War: 12
The next question I'd like to ask is, why do peaks only give a defensive bonus of 25%? Shouldn't they be the best defensive position in the game? :/
Next, do you think it's accurate or correct that cannons are fairly useless aside from for attacking towns? Just kind of weird to me. I could see where you don't want to mess with the balance too much though.
And lastly, wouldn't it be cool if the other Europeans came around to you with wagon trains and/or ships and offered to sell you some of their goods? That would be pretty amazing. Not sure if you can change this though.
Anyways, great mod, hope you take some of my suggestions to heart!