In the True Ending, it may be possible that Lunais has effectively erased everyone's free will in order to have things turn out the way she wants. First, the Evil Empire was a major event in history, so undoing that as if it never happened will have major repercussions down the line, not to mention all of the other for-want-of-a-nail events. She may have rejected everything her father stood for, but everything in the game indicates she did it out of a pure desire for revenge and not an examination of what he did wrong and why, so there's no guarantee she wouldn't make the same mistakes, and as far as we know, there won't be a second revolt should Lunais prove to be tyrannical because she has become all but omnipotent, omniscient, and omnipresent.
