What I don't like in space games, or real time strategic games in general, is that battles are usually to the death. Normally a battle is then decided when one side is more or less annihilated. Which means that fallbacks are seldom done and necessary and that the winner of a battle is often then not only a tactical but also a strategical winner, since he then has a overall supreme number of units (given equal production capabilities).
This means that to recover from a failed battle your only possibility is to build a new fleet. Because of that, the time to build ships is often quite short to make it possible to amass a new fleet quite fast, or else one battle lost would mean game over. This sometimes goes to to extremes like in supreme commander, where you don't care when you lose an army, since you can just build a new one in seconds.
I would love it if there was something which would prevent this and could make a retreat necessary (or "losing" a battle possible from other reasons then just because your fleet is destroyed).
In my opinion, the norm should be that ships are disabled, i.e. unable to battle further, instead of being just destroyed.
For example: In a battle with about equal forces on each side, after one side win, there should on the losing side perhaps be about 3/10 destroyed, 5/10 disabled and 2/10 still in fighting shape, while the winner has about 1/10 destroyed 4/10 disabled and still 5/10 in fighting shape.
The loser then would have to retreat to regroup, rearm and repair while the winner has some time to advance.
On the next encounter the winning side has an advantage, but if far into enemy territory the loser could reinforce faster so the next battle could be again quite a close match without the need of rebuilding entire fleets.
For this to be possible there would need to be quite some changes in the game (which would make it quite unlikely to be included into the game

).
First, some definitions:
-Ships are defined in battle when in a certain (not to small) area around them fighting is going on.
-Ships are disabled when their morale, fitness, damage to certain subsystems is under a certain threshold (or over it at damage).
-Morale and fitness is on a per ship basis.
-Disabled ships are unable to fire weapons and use offensive special abilities.
-Disabled ships can still be forced to fight further, but that would have catastrophic effects like accidents, friendly fire, etc.
-Ships in battle constantly lose fitness.
-Ships firing lose fitness per shot (Proportional to weapon size and rate of fire).
-Ships being damaged lose medium morale and lot of fitness (for emergency repair, wounded).
-When a ship is destroyed, other ships in battle lose some morale. (Proportional on overall fleet size and size of the ship destroyed.)
-Enemy ships destroyed, increases some of the moral of other ships in battle. (Again proportional.)
-Ships being disabled slightly decrease the moral of other ships in battle. (Again proportional.)
-Ships morale and fitness increases when not in battle.
-The effectiveness of weapons decrease proportional to a decrease in fitness and to a lesser decree to a decrease in morale.
The effects of this should be the following:
A long drawn out battle can result in a draw since the fitness of both sides is so low that most of their ships are unable to battle further. While both sides my still have most of their forces hardly damaged, further fighting would be useless. (Because of this fitness and morale are separated, since in a draw morale tends to be stable while fitness decreases continually.)
One side has to retreat since their morale is low because of losses and damages to individual ships which makes lot of their ships disabled.
Reinforcing ones fleet in battle with new fresh ships gives a great advantage since they haven't lost morale and fitness and fight with full effectiveness.
This means that it can be beneficial not to form all ships in one big fleet, but instead making two fleets where one joins the fight later, when the enemy is already broken-down from fitness losses while only half of your forces are affected.
You could stop an enemy advance by doing a rearguard action until the enemies fitness is low enough and then counterattack, with albeit a smaller force then the enemy has they can be fresh and with high fitness and morale be effective enough to halt his advance and perhaps even defeat his fleet.
Encircle some small part of the enemy forces and destroy them. The large morale hit the enemy will take should make it impossible for him to fight for the moment. Even though his forces may numerically be superior to yours he has lost this battle since his forces are unable to fight further.
Etc. etc.
To make retreats possible there need to be a mechanism so that the retreating disabled ships aren't destroyed by the advancing enemy. An easy way to this could be the following: Ships with low morale are faster, then ships with higher morale. (Running away from sure death gives quite a lot of motivation.) Disabled ships are again a bit faster, since they can use all their energy for the engines since they wont be shooting anything anymore.
A mode to move your ships backwards should also help.
Lastly ships which follow a retreating enemy should take higher damage (because of the added speed to projectile and rockets due to the acceleration of the follower and evader) and the evader should take a bit less damage (because of the lower speed of the enemy projectile and rockets and because of the dispersion of laser weapons since they would need to cover a larger distance to catch up to the evader).
Other options can be added to make retreats feasible.
Lastly damage to subsystems:
Imho 6 subsystems are enough. Weapons, Shields, Bridge, Crew, Structure and Engines.
Any time a ship is damage with a tenth of it's total hit points, or it has less then half of its hit points left, there is a chance of (total lost hit points / total hit points) that one of the subsystems is damaged. A damaged subsystem can't be used until it is repaired (which just needs some time). If two or more subsystems are damaged, the ship is disabled.
Damage to : effect
weapons : ship can't fire
shields : no shield/mitigation
bridge : no special abilities usable, high morale loss
crew : half effectiveness in all areas, high fitness loss
structure : ship takes double damage
engines : ship moves with half speed
All numbers are of course just guesses to illustrate an are to be tested.
Eventually the rate of ship building has to be slowed down, so that losing ships hurts, the AI has to be able to cope with those things and battle should be quite slow, so that ships aren't destroyed in seconds, so that there is time to react.
The overall goal of my idea is to make ships valuable, ship losses hurting, prevent battles to the death and open up new strategic possibilities without adding too much micromanagement.