Those of us who saw all the Star Wars movies as they came out have a unique perspective that won't be repeated. We had a lot of time for the SW universe to gel in our minds as being one way before the prequels and books came out (other than a VERY few books such as Splinter in the Mind's Eye).
At that point, there was nothing about the Rule of Two or midichlorians, or other things that became a factor in the prequel. Lucas had talked, though, about Vader betraying Luke's Father and the ensuing lightsaber duel between Vader and Obi-Wan on the side of a volcano even before The Empire Strikes Back came out. So we do know that Lucas had planned out some of the story from the start, as he claims.
But other elements seem to be thrown in. While there are retcon in-universe explanations, it seems obvious to those of us who waited so long to see more of Star Wars that there are some elements that were made up much later and explanations created to fit already filmed situations.
Some elements are understandable. Cheaper FX made it easy for R2 to fly, even though he couldn't fly in the movies that take place 20 years later. Adding an expiring warranty was an easy way to explain that.
But other elements don't always seem to fit with the original ideas, and two specific ones seem to be the Rule of Two and midichlorians.
It always felt like Lucas made up the whole midichlorian thing so there was some easy and quick way for Qui-Gon could test Anakin for Force sensitivity.
And the Rule of Two seemed to work in the prequel trilogy, but in the original, the Emperor discuss turning Luke to the Dark Side, Vader sees him as a powerful ally (and not in the context as an ally agains the emperor). This entire situation seemed to be written and filmed with no awareness of the Rule of Two.
While we may never know, I'm wondering if anyone has any info on when Lucas decided to add these elements to the SW universe. Did he just decide on adding them for the prequel, or is there any evidence (interviews, comments, or anything) that indicate he had these in mind before he wrote The Phantom Menace?