[UPDATE] Narrative Changes
There is audio there that is not fully
completed and will need tweaking. This is only to show you the premise of how changes in story occur throughout my edit.
As the Jedi enter the Trade Federation Ship, the storyline of Palpatine and Queen Amidala in the Senate hearing will occur in-between. This is to create a suspenseful middle-act for the movie, and to not fall asleep watching politic blabla and actually be interested in the story. Also, having changed this to a suspenseful middle-act situation also alters the story greatly:
1. The Jedi are going offensive, trying to find out about this mysterious 'Sith Lord'. Much more is now at stake and their motivations clear, because Naboo has already been taken and the Senate is already rebelling.
2. The Nemodians think that the two Jedi, dressed as the Chancellors's Ambassadors, are actually Ambassadors that Palpatine has sent to oversee them. This is explained later, and explains why the Nemodians let the Jedi enter their ship.
3. Following their escape, they meet back down on the planet with the Queen and Jar-Jar, where Jar-Jar suggests for the Jedi to follow them to Gunga City so they can negotiate the Queen's plans.
4. The Jedi swim down to Gunga City with Jar-Jar to talk reason with Big Boss Nass. After persuation from Obi-Wan, Boss Nass sees this as an oppurtunity, and tells Jar-Jar that he has brought the Naboo and the Gungans together.
All of this is cut together smoothly, and flows perfectly together.
Obi-Wan and Jar-Jar's roles now also gets significantly more important, as they play a huge part in the persuation of the Gungan Army. Also we get the feeling that Obi-Wan actually plays a bigger part now as well, as there is a lot of action for him forward after sitting out the opening act of the movie much.
I don't think it's a good idea to change the Sith lightsabers because it makes no sense. Why should Darth Vader have red while Darth Maul, Count Dooku or Darth Sidious doesn't? At least Qui-Gon's new lightsaber serves a purpose. It never made sense with Mace Windu having one either. Why does he have one again? Oh right, because Samuel L. Jackson wanted one.
In my opinion, since Mace Windu is a Jedi Guardian, he should have a blue lightsaber instead of purple or green. I would change some of the lightsabers from the background (unimportant in any Star Wars media) to yellow because Jedi Sentinels have yellow lightsabers. Maybe you could make some of the background Jedi into Jedi Sentinels as well. But, if it's too hard to correct it in the Arena battle, you don't have to do it. It's your choice. And yes, yellow is a lightsaber color. It just doesn't appear in the films or TV.
I agree with you. And the retardation of Lucas about the purpose of the purple saber is moronic. Just imagine what would happen if L. Jackson asked for Mace Windu to be incorporated as a force ghost in the Originial Trilogy. "Luuuke! Luuukh! I'm Mace fucking Windu!"
As for the arena battle and Count Dooku, all those things can be changed. But I'm not working on it now though, and I probably won't before after Christmas due to a long backpacking throughout Indonesia.