Something I have been thinking about: in TPM, Qui-Gon presents Anakin to the Council, and says he thinks he is the Chosen One, while also pointing out that the Sith might have returned. Since the prophecy is about the Chosen One bringing balance by destroying the Sith, it would seem logical for the Jedi to understand that there is something bigger going, even though they never do. This is probably due to the prophecy not having been thought out at that point, but it's another thing that makes the Jedi look pretty dumb.
So how about we change some dialogue to "You refer to the prophecy of the Chosen One who will bring balance back to the Force [and destroy the Sith]. You believe it's this boy?". I'm sure we can grab that extra bit from one of the other movies, and it would also explain what the Prophecy exactly means, which now we only learn in ROTS.
It might also be nice if we could conclude TPM with the Jedi realizing that the Sith have indeed returned and that they must train Anakin so he can destroy them, but I don't see how we could actually do this.
Any thoughts on this?