This is not on the current topic, but here are some random thoughts I had on the Prophecy and the Sith.
First of all, I like the idea of the Prophecy. It adds something extra to Anakin's character, and to the scene where he destroys the Emperor in ROTJ: he has finally fullfilled his destiny. It's a nice little tie between the two trilogies. The handling of the Prophecy is totally botched though. I don't think Lucas had even thought it out before he wrote ROTS.
I'd like what the Prophecy is to be mentioned in TPM. As it is, we don't find it what it is until ROTS, and by that time we don't care anymore. I think it could be done with some dialogue tweaks: "You refer to the Prophecy of the one who will [destroy the Sith and] bring balance to the Force. You believe it's this boy?" I think the Prophecy has to be mentioned here because Qui-Gon just told the Council the Sith might have returned, and just brought them the kid who he thinks is chosen to destroy them. The Jedi should realize here there are bigger things going on. I'd like TPM to end with the Jedi concluding that the Sith have returned indeed (as it already does), but add that they realize they need Anakin and have to train him to fulfull his destiny, and not just to throw Obi-Wan a bone.
The Prophecy is mentioned in AOTC, but the return of the Sith should be much more prominent. The Jedi don't seem to be investigating the matter at all. A scene was shot where Mace and Yoda talk about the Sith not having shown themselves in the past 10 years, but it was cut. Bits of pieces of it are on the AOTC DVD. Maybe it would a good idea to have the Jedi mention they are still searching for the Sith (maybe in the scene with the Chancellor or in a Jedi Council scene, after Yoda mentions the Dark Side is clouding everything).
In ROTS, the Prophecy is pretty prominent too. I'd like Anakin to mention it to Mace when he goes to confront Palpatine: "Master the Chancellor is very powerful. [I am the Chosen One] you'll need my help". To conclude the Prophecy in ROTS, maybe Obi-Wan could say to Yoda that everything is lost, and there can be no balance now. Yoda could say something to the effect that there still is a change for balance, and then have them discuss the fate of the twins, setting up that Luke will help his father to balance the Force. I don't really know if these changes in dialogue are possible though.
Random thought: would it be a good idea to put some Vader-shaped statues in Palpatine's office? I always imagined Vader's suit to have a bit more of a history behind it, but as it is, he just gets it slapped on. Palpatine has more Sith inspired art in his office, so it might be nice if the statues give us a clue at where Vader's suit comes from. Maybe it's ancient Sith armor or something like that.