Well if i understand you correctly, there already doing this kind of thing in Civ4 and 5 whereby faster units have a chance of retreating from battle.
I wasn't thinking about retreating, actually, though it could be added too. I mean that engine of the ship should have same impact on combat's result as armament. Faster ships will be able to break formations, flank enemy or even attack from the rear - turn their speed to advantage. Outside of simple "pursuit" and "getting there faster" roles.
In JA2 "Faster" mercs could flank the enemy to get to better position, or they could make more shots than their "slower" comrades. Yes, we in space, so cover's presense chances are reduced (you can't place your ships in "hull down" mode), but in theory ships can't have equal armour and armament everywhere, so getting to area with weaker armour or armament, or even to blind spot, to shot at enemy without any retaliation.
Of course, in fleets' formations ships will cover each other, but it doesn't mean you can't try to break that formation.
In the ancient game called 'rifles' any unit has a chance of retreating when defeated in battle, but you receive 'morale' penalties which reduces the combat effectiveness of the unit. Sometimes the units morale hits rock bottom after retreating and you are penalized by not being able to control that unit the next turn at all due to the disorganized state of the unit. It takes several turns keeping still to recover morale.
Edit: or was it called 'Age of rifles'?
I don't remember sorry, but factors of "morale", "organization", or "effectiveness" could be brought into this game too. Damaged ship could be ordered to disengage, maybe for repairs, maybe for emergency repairs, or to evacuate crew (experienced crew should be more important than ship they are serving on). Ship with low crew's morale can stop responding on your orders until it's commander will be able to restore order. IMHO that shouldn't happen with well trained crews. Organization is a bit harder to implement - part if it could belong to ship's crew's training, part to organization should reflect ships cohesion within flotilla, fleet or any other ships' formation. The higher it is, the more difficult it is to break it, the better their maneuvers are, and they are more solid as one unit. Effectiveness is derivative value, based on morale and organization (of both types).
Ships with reduced crew (do combat damages or simply as skeleton crews (for multitude of reasons, starting from lack of trained cadres to hastly evacuation from besieged shipyard) could be reinforced, but with inevitable drop in organization, resulting in some drop of their performance.
Basically units cohesion should affect their performance - if cohesion in high, then every maneuver or order performed flawlessly, whole fleet is moving as one big entity, regardless of order given - attack, turn, falling back, retreating, changing formation into most suitable one and so on. If cohesion is low, then ships will perform more like group of individuals, withh possible break outs, even collisions.
Morale could affect each individual ship's performance with possible adjustments from either commander or fleets' own reputation (sort of "it's famous fifth fleet, they are invincible!" leading to morale's boost), or actions within fleet ("damn it, they killed Kenny, you bastards! destroyed our flasghip "Chiken wing", we will revenge!", that could render ships "immoral" for some time).
I understand, on scale from zero to ten chances I see this in game are about minus two, but I wouldn't mind to add some flavour to combat.