Well, it's good to read you haraldo, cause I was thinking last night about this dark side thing, and it came to my mind somehow, Yoda repeating the phrase (EPII, I think) "the dark side clouds everything"... so, I just wandered that it could be possible that, in a certain way (being consistent with my idea of making EPIII more confusing about the Jedi's role in the Republic), the dark side, or even the Force, could be an implicit character with a will of his own, just like the ring in LOTR.
So, as the dark side "clouds everything", it makes the Jedi act wrong (or at least in a suspicious way) trying to overthrow Palpatine even if it they don't have that faculty. So the dark side, or the force, is making up a mess of everything, EVEN the Jedi Order.In this context, having Anakin trying to act on his own benefit (like I said before, making him go to Padme's instead of going straight to Windu) would be even more realistic.
This could even give a little more meaning to the prophecy stuff, since the Force and Anakin would be their real protagonists. And the movie would go on making us doubt about who's right and who's wrong even till a critical point, to then, very near the end make the watcher realize that the Sith, the bad guys have taken over
I think this was quite the original idea for the film but... it's lucas you know. So, I can't even say what needs to be done to get that feeling of what I'm talking, nor I know if Bob likes this idea, though it would be great to polish it up into something more concrete than what I posted (I mean, actual suggestion of concrete changes/corrections).
Sorry for the large post