The game is far more challanging than POTC in that skills greatly effect your characters abilities. The better than nav skill the faster you can sail however a class 5 ship requires 25 nav skill points, you can't allicat points you earn like in POTC. In COAs you earn the different skill points which are automatically added as you use that skill, so as you sail your nav skill will increase, as you get involved in battles your cannon skills and aiming skills will increase as will reload times.
You do get to earln additional points which are to help improve your character like in POTC with the personal and ship perks, you can't earn enough points to unlock all the ship perks which means you have to pick carefully and build your officers up around that of your own perks. That will add some strategy to that part of the game.
You have to build your crews skills up, they now have sailing, cannoner and fighting skills. Sailing will obviously improve the sailing skill as will firing your cannons which improve cannon reload times (not sure if it effects aiming) and boarding enemy ships will help increase fighting skill. So there are a few more tactics to that part of the game.
As for the AI, no they don't alway's sail with or against the wind and when you tell a companion to sail away its often not the way you would like him/her to sail. If you could tell your companions the direction ie, north, east, south, west then that would perhaps elliminate that problem.
The game is harder than POTC for a few reasons, but i find it more fun because of that, POTC is a great game but i don't think its a game i will play for a very long time i like COAS too much at the moment.