I've written this over on 4chan. I suppose I will be hounded by one side or the other for posting it on both locations, but I am doing such. Here you are.
The Skeksis were initially good rulers.
The dichotomy between the Skeksis and the Mystics is not as simple as Evil vs Good. The Urskeks were split in a much more complicated fashion, and that's part of the tragedy.
The world of Thra is more like the wheel of the heavens or the universe cycles of the Jains than a fight between good and evil.
From an earlier state of perfect good, Thra has been falling for some thousand years into perfect darkness (the downward spiral of the wheel, from the top point of perfect good can come only a continued revolution, downwards to the bottom). What Len aimed for in the film was a return upwards, the continued revolution of the wheel towards good and the highest point. But his conception was basic and ignorant. What he got was a return to the center spoke of the wheel; the point of perfect understanding and balance, where the illusion of 2 is dispelled, and there are no longer Mystics and Skeksis, but only Urskeks.
But make no mistake, the Skeksis are not the "evil" half of the Urskeks, and the Mystics are not the "good" half.
Rather, the Skeksis are the active, the worldly, the involved element. Action. And the Mystics are the contemplative, the spiritual, the compassionate (but detached) element. Emotion(?)
In the first age, the "perfect" age, both played splendid roles in a wonderful domain. But with time came decay into an age of darkness.
The Skeksis are active; they rule and control and kill and pillage and whatever. Their darkness is very visible.
The Mystics are completely passive, and have (for all purposes) given up on the world altogether. For the creators and maintainers of this world, that is of course unacceptable. You might say that they are fine persons in and of themselves, and disengagement is fine. But consider the difference between the Mahayana and Theravada conceptions of Buddhahood. To the Theravada, a spirit can become a buddha by attaining enlightenment. Done and done. But to the Mahayana, no spirit could possibly be worthy of enlightenment if it would go on to enlightenment but leave the rest of existence behind to suffer. It's contradictory. So how could the Mystics, given their position in the world, possibly be "good" and yet abandon the world completely? Especially when they abandon it to their more actively evil halves?
The wheel of fortune, with the king at the top and the fool at the bottom.
At the top life is grand, and all is good. But the wheel continues to revolve, and you go down to evil. (ie; 1000 years ago on Thra)
At the bottom life is shit, and all is evil. But the wheel continues to revolve, and you go up towards good. (ie; during the film)
The only stationary point is the hub. A difficult concept to describe in spiritual terms. It is a point of perfect conception and understanding. But suffice it to say that the hub is the Urskeks.