An idea i'd really like to see realised is the possibility to board with two ships (one from each side), this way brigs which have a relatively high crew number and as such make for excellent buccaneering vessels could try to take on bigger slower ships.
I just think it's really hard to program this if it's even possible ^^' ... since i love ship battles and N: TW is the only game that has come anywhere close to achieving a high quality naval combat i'll try to think of things that could be added to a mod.
Good luck with your mod in any case!