A nice compromise would be to have engines be able to be rotated to give you the ability to make sudden stops and evasive maneuvers by diverting the power from the rear engines to the engines you would place in key locations along the bow, port, starboard, ventral, and dorsal sections of your ship. Thrusters can still be used for gradual slowdown and rotational changes along the three axis of rotation from the center of your ship.