kigmatzomat
Legend
I'm curious what aspect of wind's influence on naval combat you'd like to see forefronted? Something simple and generic, like "wind advantage" (similar to combat advantage in 4e) granting you a bonus to other rolls and maneuvers, and there being various ways to acquire wind advantage, would be easy. But if you try to add much more detail, you very quickly end up adding a lot of complexity.
I recently ran Earthdawn which has a distressingly vague and useless ship handling system for a game named after a flying ship so I had to write my own. One of my players grew up sailing, as in "actual sail boats", so I had to appease his instincts without bogging down the game.
Wind is a huge factor in sailing and needs to be just as relevant as terrain on a mountain. Actually, if you deal with wind in a fashion similar to terrain that could work. Crossing the wind would be like rough terrain, opposing the wind is like mountain climbing.
Then you need to account for the waves, which causes the ship to rock (at best) or pitch and heave. Even in the gentle millpond that is the Mediterranean, wave heights are 1-3 meters. In the Atlantic or Pacific it can go from 2-8 meters under normal conditions and 10+ meter waves in storms. ~20meter waves are possible, if once-in-a-lifetime, events.
Ship to ship combat in rough weather is hhhaaarrrdd. Your ship's deck is moving up and down and rocking, possibly side-to-side and forward-to-back meanwhile the target ship is also moving. If the seas are high enough, entire crews could have full cover from intervening waves.
I don't think it should necessarily be impossible in game, but maybe it would be worth considering making it very penalty laden during rough weather to incorporate a plausible "escape" route.
Oh and one small note: wooden vessels generally don't sink. They can break up, but unless they are heavily laden with non-floating cargo (i.e. spanish treasure galleons) almost never sink at less than glacial speeds.