It might be possible to bring a ship "alongside" the ship (I think it'd be a nice touch if, say, a "Pirate attack" occurred 1% of the time when travelling by ship.) Rather than area transitions, it need only be a few "jump points" for a character to jump across to the other ship. AI scripting would be fairly straightforward, I think - just a simple IF statement. Put the ships a distance apart, and then check the X (or Y, depending on the ship's orientation) distance between Object Pirate and Object NearestEnemy. If it is greater than a value slightly smaller than the distance between the ships, the pirate "swings across" to the other ship.
The other nice thing is that once this would be written, GMs could employ it as well, for a whole party, rather than an individual in transit, and it would be far easier with precompiled scripts to work with, rather than having to manually control the opposing crew (or the water-breathing Kao-Toa, or whichever...) I think, in fact, that this might be feasible. The Kraken, probably not, simply because the walkmesh problems detailed above are pretty much insurmountable.