Hello krloz, I think what your doing is awesome and I've always thought the prequels were disappointing and could have been so so sooo much better. I have some friendly suggestions that I will post very soon. I actually wrote down a ton of things in a notebook I wouldve changed about 10 years ago. I will find it and post stuff you havent already mentioned. Liked what you did on Amidala's voice and Sidious. There are a ton of things that should be changed but heres a few lines/things that have always bothered me off the top of my head.
To be deleted...
1) Anakin asking padme "Are you an angel?" this might fall under your Jake lloyd edit
which includes the "yipee" and most of what he says I guess should be deleted.
2) Palpatine telling the Neimodians "This is my apprentice "Darth maul" he will find your lost ship" The "Darth Maul" should be dropped as it is unnecessary and cooler if its left out.
3) The pod race cg characters are terrible, I like that your getting read of the 2 headed announcer the " Thats gotta hurt line" is the worst line ever uttered in a star wars movie.
4) At the end of the movie when Darth Maul just stands there and lets himself get cut in half makes no sense... This is a guy who is incredibly fast yet stands there for 3 seconds while obi-wan does 3 flips, lands.... and then swings. Maybe atleast speed it up somehow by cutting it shorter or having him atleast try to move his saber.
5) Agree that entire gungan fight should be deleted.
6) In the scene where Sebulba is trying to intimidate anakin before the pod race I always thought it would of been cool if anakin tried to force choke him because he was so angry. Obviously he is too young to know what hes doing and cant pull it off but Maybe add a slight rumbling of the force in the soundtrack before sebulba walks away a little scared as almost like sebulba felt something and was like "wtf was that?" You know what force rumble sound im talking about right?
I have to find my notes but if you like any of these ideas let me know. Again I think what your doing is Great.