When I started my latest pirate, I made two primary changes to my method of progress.
How I addressed skill points was one of the changes I made.
I only assign skill points as needed, and leave them otherwise unassigned to be later assigned as needed. I have also found that this has helped to reduce the fall off of scored reps as levels are increased. Not to mention helping to solve the problem of wanting to reassign points, by leaving them until you later determine what is most useful to your pirating ways. Don't handicap your pirate choosing to save skill points instead of using them where they may be able help, but if you dont need to use them yet, why not save them?
The other change I made was avoiding the story quest, so it did not inflate my notoriety to quickly.
Zeppers lvl40
http://pirates.teamofx.us