Very interesting. I always knew there was something seriously wrong with the way Yoda talks in the prequels, but never really went to the trouble of thinking about it in depth before. My understanding of grammatical principles is based much more on how they sound than the specific terminology of sentence structure (I can convincingly write in different speech modes without necessarily being able to describe exactly why it should sound a certain way). These results definitely fit with the sense of wrongness previously perceived, and I agree that Yoda's speech was much less convoluted and more intelligible originally.

I seem to recall hearing or reading an interview with Lawrence Kasdan at one point where he said that he was very careful and deliberate in choosing exactly how Yoda would phrase things, and what sort of sentence structure he would use. Since he was not involved with the prequels, obviously this did not carry over to those films.