Pretty much everything in here thus far works (...'cept maybe the clap...but that's for another post

.
As mentioned, speed and balance..."sea legs". High Dexterity is a must. Followed, I would say by high Constitution (to withstand those times when food or water might be scarce, not to mention the beating sun and constantly dehydrating salt air).
Maybe even a "Pirate Acrobatics" or "Pirate Tumbling" skill with defensive as well as offensive applications.
Allow for weapon speciality with: cutlass, rapier, knife-fighting, belaying pins (treat as sap and/or club), grapple hooks, whips, and "special unarmed combat" (fists, brass knuckles, use of a peg leg or hooked hand in combat)...and if the campaign/world allows for it, I suppose throw pistols in there too.
Allow duel-wielding. Any pirate worth his salt can fight with two weapons... or fight with one and be able to do something else with his other hand.
Rope-use, swimming, boating/shipcraft, navigation/astronomy as automatic "skills" of "proficiencies" whatever your homebrew uses.
"Pirate Lore" skill or proficiency. I'm thinking in terms of the old skewl Bardic Lore ability. Pirates go LOTS of places and pick up tidbits of LOTS of knowledge, legend, gossip, etc. Ancient treasures, lost cities, secret coves/waterways, forgotten civilizations and a general knowledge of various seafaring deities, supernatural creatures and superstitions of far off lands are all in the purview of the pirate.
...Think that's all I have on this.
Have fun and happy pirating.
--Steel Dragons