I really like the retreat function in Endless Space. In short you don't automatically retreat. There is a small calculation that takes place. It weighs up the ships specs ie, light, medium, heavy and also how many ships are in the fleet. It also weighs up technology and the ships that the fleet is in combat with. So I think one awesome feature to consider adding in the future would be a retreat option if you had:
A ) Required technology researched (i.e certain engine/warp drive).
B ) Also dependent on how large the fleet is. If the fleet is over a certain size it can't retreat.
C ) If the fleet has already been damaged or not.
D ) If there are any movement points left.
It doesn't need to cause games to drag out because if you are worried about doom stacks as someone mentioned earlier, you simply lock the retreat function out to fleets over a certain size. You could end up with many more smaller engagements which would make combat more meaningful in my opinion. I don't mind the combat as it is but it would be cool if fleet size and strategic locations factored more into combat. Or also maneuvering so your fleet can live to fight another day and not instantly lose your hard earned ships instantly to a doom stack.
EDIT: It would also make ship design so much more meaningful. Imagine that your opponent as in the example above had many small groups of fighters and you just had 2-3 large doom stacks. You would obviously want to custom design the ships in your doom stack to have larger engines in sacrifice of huge weapons stats. Anyways my two cents. Just looking at providing some input and improving the game I love