Well, I've always loved the idea of Freelancer's capital ships using a more newtonian-esque manuvering scheme due to their size. The fact that WHY485 pulled it off already speaks to the fact that it can be done.
Perhaps a combination of the two of a Gravity-Rudder system (and possibly a conventional thruster on certian ships) and the addition of a heavier, newtonian physics setup a-la Nexus could make capital ships and large transports maybe differ from smaller fighters and (hopefully) give a smoother means of combat.