Weather, once implemented, will have two major impacts on the sailing system. The first is wind, which will affect the speed and acceleration of ships. Going into the wind is harder than having it at your back. 3-point sails (lateen rigging) will find going into the wind and at angles to it easier than 4-point sails (square rigging), but will not get quite as large a bonus from having it at their back. The other effect of weather is storms. Your ship can be tossed about on the waves, turned by them, and those without the training to lash themselves to the ship may even be swept overboard to their death in rough enough seas.
Which brings us to currents. Just as our world has currents that make certain routes more efficient, so too will Lithmeria. They will be modeled on the same principles that create massive currents in our world, like the gulf stream. A captain who masters both the winds and currents will be a much more efficient sailor than one without the experience, and this will factor heavily into ship combat.
Finally, we will be adding sea monsters to some of the less traveled parts of the sea. Monsters will attack passing ships and will come in varying shapes, sizes, and dangerousness. These areas will be roughly organized into "bashing waters" of various difficulty. Slaying a sea monster will give experience to all those on the ship who assisted in bringing it down. This provides a fun alternative to standard bashing as a way for teams to level, and allows those of wider level ranges to contribute together more effectively.