gethedgical,

That sounds like a very exciting and ambitious plan. I think you're asking the right questions and going in the right direction.

Here are a few suggestions:

Your idea of removing or severely reducing Yoda's role is interesting. If anything, it might make the Jedi seem more like a mystical band of protectors instead of a bunch of social workers with super powers.

I always imagined the droids would be part of the prequels. I would like to see them stay (but not the way Lucas had them).

The bad guys in the Clone Wars should be the clones and/or their creators.

How about actually showing how Kenobi served Bail Organa in the Clone Wars.

Give us some surprises. You could see everything coming from miles away in the PT. For this reason, I'm not sure the dual Palpatine/Sidious approach would work.

More Tarkin. Governor Tarkin. He seemed to know Obi-Wan Kenobi in the OT.

If you're going in the graphic novel/comic direction, I think it would be a good idea to use as much of the "look" of the PT as possible, including ships, planets, etc. That way, it will feel more familiar and we can all imagine that this is the real movie.

And that reminds me, use some Y-Wings in the PT.