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Pretty much what Max and Sarah said.
Here is my general understanding/approach.
If your a PVP'er you will want your weapons as strong as they can be as quickly as they can be, so you will want to apply the skill points to the various weapons skills to do so. This will slow your ability to gain additional reps and further level your pirate/weapon as you continue to progress (because you get fewer rewarded reps)
If your a questing type you will want to reserve using available skill points to maximize the amount of rewarded reps you get as your pirate continues to progress. Apply skill points to obtain new skills, but not to further strengthen those you already have. (one exception broadsides on sailing.. fill'em up)
Playing a combination, then some form of a happy medium loosely using both options would probably be appropriate (at the pirates own descretion).
My level 38 pirate has 1 point on everything that became available, and only a couple items in the whole scope of things with more than 1. Passive skills are generally more useful than the individual skills as they often effect more than one weapon.
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