Well I use flails to hold the shields down of large ships until the marines get onto deck 1, after that you do not need to fire any-thing. Flails are also good for cannon folder too, and feel improve the odds of the marines reaching the ship unharmed. I did notice that large ships need their shields under 5%! which is fairly easy with flails - although takes a quite a lot of them.
ps. I do remmeber Multi Vector mode from star-trek. It was great seeing it although I always wondered if the ship wasn't stronger as 1 ship?