I like this idea, but I just wish cannons could be on moving ships. It would be cool to see cannons firing and damaging the ship slowly to the point where it sinks, and there are explosions, fires and crap like that. Unfortunately, game engine or something along those lines people begin to blame it on not being able to be added. But yeah, if we can't have cannons, at least let muskets do damage.
I personally don't understand how a few cannons can't be added to the schooners, but im no programmer (yet) so i can't say for sure whether it can or can't be done.
As for boarding, I agree, maybe we should have ropes that we can shoot to attach to other ships, if you hit the ship with a few ropes ou can start pulling it in.