First of all, I really like what I'm seeing here with SK. Good job and good luck
In symmetric games, difficulty levels are typically simple bonuses: extra hitpoints, more production, etc. I think they get pretty boring after a while. You can only add them for a while before the game breaks. And AI is at full capacity very early, you just can't beat a good human player on level ground - at least without a heavy investment of man/froghours.
I'm wondering if the asymmetric nature of SK could be taken advantage of to create more interesting difficulty levels. I don't know much of the design, but I'm thinking of either handicaps that affect only the player, but fit the story well. Or extra advantages given to SK that are not so blatantly obvious as, say, extra hp. I'm afraid I can't name many good ideas right away, but I hope I'm making at least some sense.
As an example the good old "AI knows where all the colonizable planers are", but in a way that keeps immersion since SK has far different resources at his disposal.