This is the one bit of design I've actually already done...well, sort of, anyway...ship-v-ship combat using mounted tween-decks ballistae to replace cannons.Seriously, though, hardly any, you would need to add some sort of specialized combat system for ship battles, depending on how historical you want to get with them.
Good point [MENTION=19675]Dannyalcatraz[/MENTION] regarding weather magic; that would have to be reined in (though not necessarily eliminated). In fact, most ranged spells become problematic sooner or later in this milieu - even a simple Hold Person on another ship's helmsman could ruin its whole day, along with that of the third ship it then crashes into.
Is the answer then to somehow make casting from shipboard very difficult - e.g. a very high chance of failure unless the spell targets only the caster or something the caster can reach out and touch?
The other aspect that really gets in the way here is non-standard PC means of travel - flight, teleport, dimension door, etc., particularly by device rather than spell.
Yes - things like ramming, boarding, and on-deck combat are already easy to handle. It's the ship-v-ship stuff, and somehow being able to break resolution out to that scale (which for one thing is much slower - each ship-v-ship combat "round" might well be several minutes long) while at the same time being able to account for PC actions.If you just want to do a Pirate Movie kinda Age of Sail, though, the action will usually come down to boarding, anyway, and the kind of relatively small-scale combats already familiar in D&D.