First of all, excuse if anywhere all of this was already posted, I've been looking for this topic for some time and wasn't able to found anything even vaguely related to it. Ok, now on topic.
For quite some time, there has been a lot of tallk about the fact that Paladins wouldn't be a good choice for this AP, but personally I've been always more concerned about the possibilities of playing a Cavalier in the AP. Having a product like 'Pirates of the Inner Sea' in schedule I was waiting the chance that there might be some sort of piratey archetype for the Cavalier that would allow to play one in the AP without much problem. But there wasn't, so I waited to see what the Player's Guide said about playing Cavaliers, but the class-specific section was cut out in this one.
So, to sum up, if you wanted to play a Cavalier in the AP, a class with some abilities (Tactician, Banner, Challenge,...) I think would make quite an interesting pirate captain you would have to endure having quite some options that would almost never be used and felt against the spirit of the AP (namely, all the mount-related stuff). Right now, as far as I know, there are only 3 archetypes that wouldn't burden you with a horse in a ship, but all of them have, as I see it, their own problems, Musketeer (firearms usage problem), Sword Saint (too narrow on focus), Beast Rider (so you can ride an aquatic or flying animal, but, again, too narrow on focus).
Personally, I think that would be nice to have some archetype that gave you something more piratey instead of the mount-related stuff. For example, with the addition of the ship-to-ship rules, I think that something could be done with that. Even if it's not in the first chapters of the AP, there could be space in the late ones or maybe as a blog entry. I don't know, just my 2 cents.
As english isn't my mother language, I hope everything is clear enough to bring my point through
Is 3PP allowed? Rite Publishing’s Secrets of Tactical Archetypes 1 has an inspiring commander cavalier archetype that replaces the mount for party buffing capabilities. That plus the Order of the Cockatrice would work very well for a pirate captain, imo. Grab a cutlass, don some light armor, and start bragging and ordering around! Disclaimer: I'm the author.
If I go cavalier for Skull & Shackles I'm gonna go with Standard Bearer. You get the Banner ability at level 1 instead of the mount, which I think will probably be more useful than a horse most of the time. That being said, I don't think the mounted cavalier will face any more problems in S&S than they would in your average adventure. If nothing else, get someone with Knowledge: Engineering to rig up some kind of harness that will allow the horse to assist in rowing or something.
Can the sword saint archetype (dragon empires primer) for samurai apply to cavaliers, they're close enough to each other (samurai being an alternate class for cavalier and all) that way you don't have to worry about a mount and be a total bad ass:)
That much like everything else would probably be up to the GM. But I personally have never had a problem re-skinning some mechanics so they could be used in a different environment. I can not think of any reason balance wise why it would not work.
I think Banner could be easily tweaked for S&S:
Skull and Crossbones:
Whenever your ship flies the Skull and Crossbones in battle the crew receive a +2 morale bonus on saving throws against fear and a +1 morale bonus on attack rolls made as part of a charge. At 10th level, and every five levels thereafter, these bonuses increase by +1.
It gives a bonus in boarding actions, which will presumably be a fairly frequent occurrence since there are naval rules, but doesn't help on land.
I haven't read the naval rules yet but I imagine someone will come up with a class feature that could help in naval combat and replace Mount.