Trimming what he says can only go so far.
Jake Lloyd's delivery of even reasonable lines is as grating as anything Hayden says.
Anakin should have an English accent to match Seb Shaw and should be more subdued, still lively but not cute in that annoying petulant child actor mode that bugs most films with young characters (more Pan's Labyrinth than Jingle All The Way).
If you start the film on Coruscant you don't need the scene in the Gungan city because Qui-Gon and Obi-wan need never go there.
The Naboo know about the invasion because it's been happening all around them.
Some of the elements of those scenes could be cannibalised for later though.
The story needs fixing before you even think about the visuals so doing a rough work edit to prove it can be done makes more sense than worrying about the colour palette (though that does need fixing too).