I think the game should have more crew killing ability. so there's more than one way to win.
outright destruction should not be the only option, hell it should be the worst option. if you take the ship, you can sell it.
when cannon shells go through armor, they should fragment and bounce around inside the ship, killing the crew and destroying ammunition storage.
with this, there would be new possibilities. weapons, of course, and a medical system. having a well thought out and easy to traverse ship means injured crewmen can get back in the fight faster.
and have players need to think about angling their armor so shells bounce off. also, switch the cannons. the big one should be a big kinetic punch while the small canon penetrates better and fragments inside the ship.