If I were to redesign the game from scratch, the Proton Torpedo would cost 2-3 points, require a TL and focus token, and roll only 2 dice.
On hit: the defender suffers 3 critical damage (4 if a large ship).
Similarly: missiles would roll lots of dice, but deal only a couple points of damage to large ships, but a few to small.
Granted: this wouldn't really work in the current format, as there are several 2-3 agility large ships flying about. And my Proton Torpedoes would devastate Y and B -wings.