Uncle G just thought it sounded cool.
That's it.
And when you rely on things based solely on the idea that they sound 'cool', they tend to cause more complications than revelations.
This prophecy element in the prequel story line is one of the most inconsistent and poorly thought out additions to Star Wars. Not simply because they added it in, but because it just wasn't handled well. Let me try to explain.
Qui-Gon: He was trained in the Jedi arts. My only conclusion is that it was a Sith Lord.
Ki-Adi Mundi: Impossible. The Sith have been extinct for a millennium.
Ok. The Sith have been out of the picture for a thousand years. They've been gone for so long that the Jedi think their reemergence is out right impossible. If that is the case, why do they still keep the prophecy? As Obi-Wan states in Episode III-
Obi-Wan: Is he not the chosen one? Is he not to
destroy the sith and bring balance to the Force?
The prophecy seems to specifically state that the Sith need to be destroyed AND bring balance to the Force. Unfortunately in Episode I, none of the Jedi put the two together.
Mace Windu: You refer to the prophecy of the one who will bring balance to the Force.
Now, I don't know about anyone else, but if the Sith were a part of that prophecy to begin with and the Jedi know it like it was common knowledge, why don't they put the two things together? For the first two episodes, no one associates the Sith and Anakin's 'chosen one' status as one and the same. Why? Because they never were when it started out. If you listen to Lucas in his Episode 1 commentary, he states that Episode II would delve deeper into the whole prophecy storyline. And how did he make on that promise?
Mace Windu: if the prophecy is true, your apprentice is the only one who can bring the Force back into balance.
That is all that we ever get out of the prophecy in Episode II. If you want a bonus round, he also states in his Episode II commentary that he was going to reveal who deleted Kamino from the Jedi data banks in Episode III. What do we get instead? Well, in his Episode III commentary, he simply says "Audiences should be able to connect the dots that it was Dooku." Oh, thank you George. I came up with that idea long before we were introduced to Dooku since he's a rogue Jedi and all, but since you tried to keep it a secret and not reveal it till Episode III, I just assumed you were going to be creative for once instead of resorting to the blatantly obvious. :unsure
In the words of Plinkett:
Plinkett: "You see, A guy named of William Shakesman once said, "Brevity is the soul of wit". This just means don't waste my time. You keep it nice and simple....I said stop wasting my time! Stop it!
So in conclusion, Lucas didn't know jack about the prophecy and just stuck it in Episode I thinking that it will somehow play out as the story progressed. Unfortunately, he didn't write that story, and in the end just said "fu** it" and wrote the "destroy the Sith" so everyone will think that killing Palpatine somehow fixes everything.