The idea is simple: have the option to liberate systems from factions which conquered it from a third faction. 


It is not always in your interest - at the moment at least - of increasing your amount of systems due to internal costs in money, vulnerability, politics (capturing Sophone inhabited systems will irritate the Vodyani's tendency for religious laws), etc. Yet the aim of the war should be to weaken your enemy. One way to make war balanced is to have the option to liberate systems. 


To illustrate, suppose the UE is becoming inreadibly powerful. They have recently annexed the entirety of the Sophones. You, as the Vodyani, being religious, are not keen on capturing the former Sophone systems. After all, the increase of Sophones may shift the elections to scientist. And perhaps you want to win the game through other means than domination. Or maybe you simply can't afford the drop in approval from too many systems. So an option should be to weaken the UE by liberating former Sophone systems and returning it to the Sophones. This way you weaken the UE, rebalance the balance of power in the galaxy, and gain a new friend. Liberating systems long after the war should also be an option.


P. S. Related but unrelated, ES2 needs a sort of warmonger penalty. Is it just me or doesn't the AI care if you are starting to dominate all his friends? Liberating systems will counter warmongers while lestening your own warmonger penalty. 


tl;dr: You should be able to play as a galactic policeman.