Just watched your newest clip, and it looks great, but I do have a few suggestions.
1) The silence used to remove Palpatine's line about Grievous is a bit awkward. I guess it's just a temporary solution, but I thought I'd point it out all the same.
2) Like jedi_jra already said, you should keep the "I need him!" line, which I think should be easy enough to do
3) Intercutting shots of "emperor" Palpatine with "normal" Palpatine... It's a great idea, but not very "Starwarsy". I suggest just having him change into the emperor without any further explanation, but it's a tricky problem.
4) I think the line "what have I done" should be kept in, although I know many people will disagree. It makes the turn just a bit more gradual, in my opinion, but I understand why some people dislike it.
And now for something completely different... Your title "The Dark Times" is a bit too vague for my tastes (so are "A New Hope" and "The Phantom Menace", come to think of it). My personal favorite Ep. III title is "Fall of the Republic", but in the end it's all up to you, of course. (By the way, in case you were wondering, my Ep. III edit is not quite dead. It's more alive than my current computer, anyway. So once I save enough money for a proper computer, it's back to editing.)
On the whole, your edit looks really great, and I'm really looking forward to seeing the finished product. Will it be 5.1?