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.
Sail
As you buy more and more crew from the Tavern, you will get increasingly good perks. Usually the Bronze perks will be switched out rather early, and it's inadvisable to upgrade these perks. It's when you get the Silver perks that things starts to be really fun - some Silver perks are my absolute favourites (High Spirits, for example, and Ship Collision is amazing in the pesky fort-raiding missions). Those Silvers were used for such a long stretch of time and only replaced by the 500.000 and 1.500.000 Legendary perks. Some Gold perks, like Rage, are only good in theory and rendered useless by bad placement - by the time you are strong enough to get Rage, you don't need it anymore. I never equipped Rage even once - when I got it, my ship never got under 30% in combat anymore.
Don't bother upgrading the Bronze Sail perks. Just...don't, not worth it.
Gold:
- Boost
- File Seeker
- Rage
- Minesweeper
- Dynamic Event
- High Spirits
- Ship Collision
- Discretion
- Expert Seaman
- Iron Sails
- Fog Expert
- Night Vision
- Stay Alive
- Liberator
- Fog Range
- Wind Down
- Wind Up