It does definitly come down to skill, both flying & strategizing. I have a medium difficulty mission which involves 1 on 1 Onslaught battle, evenly matched. Its possible to win taking less than 50 armor damage (because of all the asteroids, my lowest damage number was 23) using smart tactics and good timing to out maneuver the enemy Onslaught and get all of your missiles into its rear (as Onslaughts have only half-coverage shields, and their PD only covers the front 270 degrees, leaving the engines totally vulnerable.
I have a hard difficulty mission which conversely is very much strategy oriented. But once again, with some good planning you can come out victorious. I've found I can only get 86% (and that was once only), compared to 87% and 100% for the two stock hard missions.