Um.. so I beat the final boss, but two of my party members were dead. Not only do I not get to talk to them on the ship at the end, but I also don't get to hear about what becomes of them in the end credits? what the heck is up with that? that's not fair....

Cast the ghost vision spell, their ghosts should be on the ship. You don't hear what happened to them because they died. But yeah, it is a little silly. You just have to keep them from dying in the fight.