What I want to do with the IKS, is have the players take a role in freeing the planets that the IKS have taken control of. As freetraders, they can work within IKS territory. I'm going to have them become involved with the resistance on one of those subjected worlds.
I also want to have the events of this era and the actions of these characters reverberate into the 24th century, eventually leading to Baker's Dozen joining the UFP. Which I'll deal with in my 24th century campaign.