I admit I haven't gotten any of the official booster packs yet, but going by the teaser rules and the freebie ship in this month's Scrye, this looks like a fun game. I'm a pirate fan and have been looking for the perfect game for capturing the pirate'y feel.
Pirates Cove comes very close for me, but lacks the direct conflict and swashbuckling that would take it over the top - the roll of the dice takes the place of a real combat. Now, we have a more hands-on conflict resolution system in PSOM. Wouldn't it be cool if we could combine the two?
In order to use Pirate's Cove as a campaign system for PSOM, players could all start with a 2 mast ship. As you buy new cannons and sails in PC, you could then add masts to the ship you use in PSOM. Adding crew in PC would mean characters added to your ship in PSOM. Adding "master" cards in Pirates Cove might translate to a "+1" to your die rolls, or a 'free re-roll' type of thing during your PSOM combats.
Anyway, just some quick thoughts. I hope to try it out - if I can actually find any boosters of PSOM! If anyone gets to try this out, please let me know what you think!
Battle is still determined by a die roll in PotSM, so I'm not sure you'll find it any better.
I do like your idea of somehow combining PotSM and Pirates Cove though, as long as everyone played with the same ship.