If anything, this game is more like a sequel or sidegame to Patrician III. It is most definely NOT a sequel to Port Royale, even though the basic premise is the same. From memory, in Port Royale you had the same kind of objectives, but it was much much much easier to turn rogue and run around sinking ship 'Pirates' style, then it was to fiddle around trading.
Still a good game, if you like Patrician, but not the game you're looking for if you like being a pirate, as it only allows you to control 1 ship in battle at a time, no matter how many in your fleet, nor how many attackers there are.