There are a lot more perks than ships and frankly a few are rather useless even from the beginning, so I will only comment on the ones that I used throughout my conquest of the Caribbeans.
In this post schedule: Perks, comments on perks, perks progression/ in different situation, end-game perks & legendary perks.
I'm swamped by how many perks there are, so bear with me and I'll upgrade them in parts :s Sail perks are by far the most numerous, so I'll start with these first.