As I continue to think things out, go back and read/watch critical reviews of the PT, and write out some scenes, I'm starting to think it would be best to not make this the Tragedy of Anakin Skywalker.
I think RLM had a point that it should have been the story of Obi Wan Kenobi. In the OT, Obi Wan was there to pass the torch. It is more impactful if Obi Wan was the central heroic figure of the PT rather than the mentor of the hero. Especially if Anakin as main hero ends up being reckless, weak and ultimately villainous (or dies an ambiguous death for those of us trying to preserve OT surprises) before simply being cool villain in the suit for most of the OT.
Anakin will be a tragic figure no matter what, at least when unveiled in ROTJ. But to delve into his downfall for 3 movies, just to spend another 3 movies to get to the resolution, to me, falls flat. Should we be led to dislike Anakin as central hero in the PT or be rooting for Vader in the OT? Or have mixed feelings about the whole affair? Ultimately I don't know if the exploration of how Vader became Vader is that interesting - aside from him being the father of the OT's central hero, Luke.
Alternatively, the central hero could be Luke's mother. Her character is a blank slate. She could be a strong character, urging Kenobi to take her son away where he would not be found. It is through her that Kenobi gains importance as caretaker. [Not sure how to deal with baby Leia yet].
I agree very much with sentiments expressed in McFlabbergasty's last post. The PT should be able to stand on its own. In passing the torch, Obi provides the link between the two sagas.
I don't envision Palpatine leading the Senate or engaging in lightsaber duels. I think he will be spoken about, his manipulations implicit in the actions he takes and the power he gradually builds. I think I will show him rarely, if at all.
I'm struggling to deal with Bail Organa's place. I see his storyline as separate from those of the main heroes most of the time - yet he is an important figure.