Back to busiess, as it were, MTHaslett once again has excellent input. I'm in agreement on pretty much everything, except for the replacement of Across the Stars with the Han & Leia theme. AtS is an excellent piece and fits the romance appropriately. Han & Leia's theme belongs in the OT...with Han & Leia. But other than that, listen to him TM!

"Obi-Wan's going to burn me alive." *cringe* I think it would best to leave only Anakin's sigh of frustration in reaction to his broken lightsaber. No in-joke one-liners please.
Qui-Gon: I've been thinking of ways to expand his role in the saga, as he is also my favorite charcter in the prequels (Liam Neeson is also my favorite actor). A good source would be the Episode 1 tone poems (I've mentioned these before in one of Obi-wanton's threads). I don't know if you're familiar with them, but Qui-Gon's goes as such:
It will be a hard life.
One without reward. One without remorse. One with regret.
A path will be placed before you. The choice is yours alone.
It will be a hard life, but you will find out who you are.
I have several idea on how to utilize this. One being during Qui-Gon's funeral parts of this could echo in Anakin's head. However, based on how you are handling his dreams, they would be an ideal place in insert the voice of Qui-Gon. Perhaps in the first dream quote "It will be a hard life," and in the second, include the complete first and second lines. Then in RotS, during the ruminations sequence, the third line. along with some spliced dialogue, "[You are] [the Chosen one]." I'm getting a bit ahead of myself here, but you get the idea.
As far as the overall music goes, I'm really excited to see how your alterations it into the film, as music (especially in Star Wars) can make a HUGE difference. Though I like the choice of "Uranus" as Dooku's theme, don't you think it's a bit bombastic, and is bound to get repetitive after awhile. Although you might have all this worked out already and rearranged it. Either way I think this merits more discussion.
You mentioned rotoscoping lightsaber before; I would love to get a screenshot of your attempts. I'm going to soon have After Effects, and the first thing I'm going to play around with is rotoscoping. Mace should have a blue blade, definitely. Now I've always thought Dooku should have a purple blade for quite a few reasons:
-Variety. Jedi: Blue and Green, Sith: Red and Purple.
-Symbolism. Dooku is a mix between Jedi (blue) and Sith (red), which of course makes (purple).
-Royalty. As Sam Jackson often reiterates, purple is the color of royalty. Dooku is a Count after all, so there's a connection there as well.
I know it would be a pain to rotoscope, but if I ever figure out what I'm doing, I'll do it myself anyway. The ONLY disadvantage would be in RotS when Anakin takes Dooku's saber; as it stands now he holds in his hands the balance of good and evil. I'd really hate to loose that, but if we're reinventing the charcter of Dooku the lightsaber is a good place to start.
I believe we've discussed before the subject of Dooku being or not being a Sith, and you sided with the official scenario. There are various advantages and intriguing story points to both, but especially with Dooku no longer using Force lightning, it would be all the easier to make him a rouge agent of the Force. This ties into my editing wish that Grevious=Maul, but that is for a later discussion.
I don't have time to expand on the logistic of Queen Padme Amildala, but I will I get the chance.
What I've been keeping in mind, and I hope we all will, is that Episode 2 in whatever form it mayt be needs to be able to fit into Episode 3. We all have our ideas on what to do with that film as well, so before setting into stone anything in this one, we should consider how that will impact any alterations we'd want to make to the next one. The goal is to not only make everything more like the OT, but to enhance the prequels into a tighter trilogy and story of its own (which will help along the former objective as well).