There are several things such as even the 40 points fleet limit that leave me wondering what the original idea was for how they thought the game would be played. Did they want fleets with only 2 ships? Did they think people wouldn’t use crew as much? Did they mean for players to be able to stack loads of Unique Treasures and only have a few actual treasure coins?
In the original set, the standard fleet size was only 30! Two-ship fleets and treasure pools with just 2 or 3 UTs (total) were pretty much the norm, although back then it mostly worked just because there wasn’t a whole lot available, and what was available was relatively well-balanced across the three nations (Spanish, English, and Pirate).
In my opinion, I think that the game wasn’t really ever designed to be played super competitively and as more sets were added unintended combinations, stacking effects and abilities crept in unmonitored that lead to certain things being at a power level way higher than was expected, which is why I personally avoid some of these things.
That’s not even an opinion – that’s exactly what really happened. The original game was just meant to be a once-off “beer & pretzels” game to see if it worked, and the rules were purposely written loose so players could easily modify it to however they liked. Even Wizkids was blown away by the game’s immediate success, and they had to rush extra printings early on because it sold out so quickly.
There were no tournament or organized play rules for it at all, and nothing was even planned, but there was so much player demand that they had to quickly pull something together, largely by modifying the tournament rules from their other games like Mage Knight, Mechwarrior, and HeroClix. The problem is that there’s always been a large disconnect between the precise, formal rules necessary for a competitive tournament setting and the game’s inherently flexible nature, and not enough effort was put into it (especially in those early days) to close up that gap, which is why all these years later we have a 50+ page FAQ to deal with everything.