Currently training/grade does not do much if you use missiles. It would be nice if the effects of low grade/training were increased. An easy and awesome way to do that is to add panic system. Crew gets scared when they take damage, or see friendly spacheships explode. This is mitigated by crew training, crew grade and commanders. Too much panic = random effect (ship tries to flee towards nearest jump point and away from biggest enemy ship, or ship shuts down engine or ship takes random internal damage)
Then their morale resets when they get their crew leave.