[Jubala]

I agree it wouldn't be much fun being pounded to scrap by longer ranged enemies, but if that's the case you better get longer range or higher speed yourself asap. And a ****load of pointdefense if it's missiles we're talking about. As for catching marauding enemy fleets you have to do it with fast ships and/or fighters. Arm them with enginebusting weapons and they'll be slowed enough to let the big boys catch then.

I'm not saying that you should have automatic disengage the instant the desicion is made. It should take some time depending on the speed of your ship and maybe range to enemies. Kind of like in Stars! where it is possible to disengage but not certain it will succed. Or Reach for the Stars(I think that's it anyway) whose only redeaming feature was the ability to sacrifice your screening escort ships to save your capital ships. I just find it so annoying that my single cruiser has no choice but to make a suicide ramming run on 5 dreadnoughts because it can't run even though it is faster. Or for my capital ships taking a pounding retreat to fight another day. Or at least attempt to.
The ability to run would place a higher importance on smaller faster ships to pin the enemy down while the big boys move into range. Or block the enemy to let your bigger slower ships get away. I think it can done so it's balanced and playable.

I don't want it be like in Star Wars Supremacy (Rebellion) where the enemy instantly hypered out if the force concentrations was even slightly against it. I want it to be possible to run but I also want it to be possible to catch runners.

It could also be coded into the AI behaviour when it decides to run. Aggressive AI's would linger longer while cautios AI's would be more prone to disengage and fanatic AI's would simply bull in and take it.