Well, just a thought, but maybe you could give the ships action points, so for example, a Perseus might have 5 action points, it can either attack for 1 point or move 1 sector for one point? That way a Perseus can 'Intercept' e.g. 'Move, Move, Move, Attack, Attack' or, when in combat with another unit at the start of a round, it has 5 attacks.
Other ships may have lower attacks, but do more damage per combat round
This means something like a Corvette would have 2 action points, as would a Destroyer, it can enter a system and attack a target once in a turn, or attack twice while in combat, but it hits DAMN hard!
The only downside to this system is that it does not account for manouverabilty of fighters, so a Corvette is just as likely to hit a Squad of Ulysses with it's main guns as a Shivan Cruiser (Though you could probs do something with subtracting one ships AP's from the others). You might find that Capital Ships will need 2 firepower ratings, Anti Capship and Anti Fighter.
Just a few thoughts
Flipside
