I think a modified version of the EU4 system would be nice. Warscore should be easily researched/reduced so it only matters if you don't achieve a decisive victory. So it would be possible to take over huge swathes of territory after a 100% victory, after all that's the equivalent of unconditional surrender (maybe tweaking that score a bit so wars last longer and are bloodier).
But afterwards, holding the gains would be a real pain, the occupation draining your economy and your political power, while fueling unrest everywhere (rebels in the occupated territories, separatists in other sectors, isolationists and disgruntled former soldiers in your core territories etc.). If you bit off more than you can chew, your whole empire could fracture. And while you're integrating new territories, it would be unwise to attack again, creating a more dynamic and realistic "truce" than the current system. Breaking a truce should be possible if you have the economic power and if you can take the diplomatic fallout.
The severity of the penalities should be directly tied to the empire's ethos and most importantly its own population compared to the population now being incorporated. That way, an OPM struggles with one planet, while a sprawling empire easily takes over smaller opponents and large blocs can reshape the whole galaxy in one war.
A system like that would better show the problems that come with annexing great numbers of foreigners in your empire, while on the same time scaling with your power. Also, it would allow much more dynamic developments then currently, where big blobs rarely fracture. Finally, it would allow more strategies against the big blobs. Wait till they are engulfed in annexation-efforts and then help the rebels while invading etc.