Limit total number of points per officer to 6 points. That way a combination of skills must be attempted or a unique 6-Points skill spent.
Give the Pirate Hunter, Pirate, and some other perk use 6 points they either become unused or make way to specific gameplay.
Also, as Otto puts up, fleet absolutely murdered all "historical" and credible pirate play driving the pirates even more down the nation line.
At least during the past after the removal of AI reinforcements there was a drive towards small ships raiding trade, solo or in small groups of 2 and 3.
Now piracy, as everyone wanted it, is dead and Pirate Nation is back to full black nation copycat with no more interest in going in a sloop, schooner or brig out there to intercept trade.