Since the inception of the new Merchant Marine reputation system, I've redone
the formulas on Combat-Based alignments (pirates and navy), specifically,
reducing/removing the penalty against smaller ships, and increasing the
benefits. For those who would like a little bit more control over their sailor
reputation gains, these alignments should be a tad more appealing.
Additionally, don't forget that for Navy members, there's a sizeable
reputational bonus for seeking out and sinking bountied ships (list available
at the Silverlake bounty office).
With regards to the current issue of 'regain' for Merchant Marine-aligned
sailors, I'm currently working on the issue.
Finally, sometime in the next few days, I should have the issue resolved
regarding the exp-tuning applied to the generic sailors.