Wow! You should collect all your ideas into a single work and share it; I'd love to read what you have!

You mentioned Yoda's role, and I wanted to say something about that because I had an idea. Personally, I don't think we should see or hear Yoda at all, at any point. Yoda's reveal in ESB (and the drama/emotional context involved) should be intact, or even enhanced by the prequels. The point of Yoda was to illustrate an important detail about the nature of the Force; that "size matters not" and that it's something beyond the physical. Luke was expecting Yoda to be this great big warrior dude, but he was actually just a little guy.

I think the prequel characters should talk about Yoda a great deal - add to the mystique, so the audience keeps building a mental image about Yoda being this big, majestic, super-heroic figure. Yoda-this, Yoda-that...which makes the impact of Yoda's appearance in ESB all the more poignant. When Obi-Wan tells Luke on Hoth to go see Yoda (if you've watched these prequels), you'd think "oh man, we're finally going to see Yoda!" The excitement would build throughout ESB, and the audience's expectations (built up while hearing about Yoda in the prequels) would create a lot of depth to what you actually get: a little troll living in a shitty swamp. You're still surprised even if you don't watch the prequels, but if you DO watch the prequels, it's an even deeper experience. That should be the overarching goal of any prequel, I think.