1.) As far as Hayden and Jake go, if you realize that they are going to struggle with many lines, you should cut out all unnecessary lines from these two. The less said by Anakin the better. I think a more minimalist style to Anakin's dialogue would allow the character to blend in better with Darth Vader, who was always a calculating and efficient with his word choice (examples: "I find your lack of faith disturbing" to Motti, "Perhaps you think you're being treated unfairly?" to Lando, and "The Emperor is not as forgiving as I am" to Jerjerrod). Anakin definitey has way too much dialogue in the prequels. If Anakin were more of a minor character in the Phantom Menace and a man of fewer words, he could have been much more effective. I think Obi-Wan should be the hero of all three prequel trilogies, and the scripts should have been written to reflect this. First scene on the chopping block (one of many): "It's working, it's working!" No kid actor could have delivered this line well.
2.) Instead of putting Anakin in the cockpit of the Naboo starfighter in Phantom Menace, Anakin should have stayed with Obi-Wan and Qui-Gon to watch them fight Darth Maul. This change would have removed the utter lack of seriousness for the space portions of the battle and would have furthered Anakin's character development, by having him witness a traumatic event and be exposed to both sides of the Force. I actually expected this to happen in the movie. Lines like "No one can kill a Jedi ... I wish that were so" and "It's a hard life" from Qui-Gon hint that Anakin will be exposed to these challenges within the movie. The scene would not have required any dialogue from Anakin, but merely a few telling glances from Qui-Gon and Maul. Instead he goes off and destroys the Federation battleships and delivers the line "This is podracing". Horrible stuff. Luke's attack on the Death Star was heroic and required maturity, but Anakin's attack on the Federation ships is idiotic and impossibly lucky, not heroic.
3.) Remove the Midi-Chlorians. Qui-Gon's senses should be proof enough that Anakin is powerful, we don't need a blood test. I don't mind the Prophecy, but it would have been much better without the Midi-chlorian explanation. This change to the lore also contradicts the view of the Force shown by Obi-Wan in ANH and Yoda in Empire.
We would much rather have Qui-Gon's explanation of the Force be consistent with the explanations given by Obi-Wan in A New Hope and Yoda in Empire, but with his character's own personal touches. Here are their explanations of the Force, which is not unexplainable magic, as most people seem to understand it.
Obi-Wan : "The Force is what gives a Jedi his power. It's an energy field created by all living things. It surrounds us and penetrates us. It binds the galaxy together."
Obi-Wan's explanation seems to imply that the Force is universal. Midi-chlorians do not create the ability to use the Force, but other living things create it. Any being can use the Force with enough training, focus, and patience. Specifically, your ability to use the Force stems from your mind, not from the number of symbiotic organisms within your body.
Yoda: "Size matters not. Look at me. Judge me by my size, do you? Hmm? Hmm. And well you should not. For my ally is the Force, and a powerful ally it is. Life creates it, makes it grow. Its energy surrounds us and binds us. Luminous beings are we, not this crude matter. You must feel the Force around you; here, between you, me, the tree, the rock, everywhere, yes. Even between the land and the ship. Luminous beings are we, not this crude matter."
Notice how Yoda specifically made the contrast between matter and humanity. Yoda says that humans are more than just the sum of their cells. Explaining one's ability to use the Force through the results of a blood test means that the Force does boil down to 'crude matter'. He also repeats Obi-Wan's assertion that all life creates the Force.
The Midi-Chlorian explanation in Episode I specifically refutes the explanations of the Force given in the original two Star Wars films. In the OT, we could say that Yoda is the wisest and most powerful Jedi because of his faith, dedication, focus, patience, intelligence, etc. In the PT, we say that Yoda and Anakin are the two most powerful Jedi because they were born with the highest number of Midi-chlorians in their body. This is almost a Social Darwinist theory of the Force.
Qui-Gon says that without Midi-chlorians, life would not be possible and we would have no knowledge of the Force. Therefore, all living things possess midi-chlorians, and all living things should have access to the Force.
The film would have been superior if the midi-chlorians were never mentioned, though. The Force definitely has changed since Obi-Wan described it in Episode IV (Lucas was trying to make a positive change, but hurt the films instead). In Episode IV, Obi-Wan comments: "When I first met your father, I was amazed at how strongly the Force was with him." In Episode I, this comment seems to have changed to "I was amazed at how high his midi-chlorian count was." The descriptions from the original trilogy imply that your ability to use the Force is limited only by the strength of your mind and will. Yoda makes it abundantly clear that NO PHYSICAL LIMITATIONS can be placed on the Force, including a Midi-chlorian count. In the PT, this is no longer the case.
Lucas has treated his audience like complete idiots throughout the prequels. The audience understands exactly what Lucas is TRYING to do with the Midi-chlorians (all too well), but it does not have the desired effect. This is a clear-cut example of one of the main problems with the PT: Lucas explaining the story through expository dialogue instead of demonstrating things through action. (ie- Lucas tells us Anakin is strong with the Force through prolonged dialogue, while Luke demonstrates his strength through actions; Anakin and Padme tell us their feelings in words, while Han and Leia demonstrate their feelings through actions and expressions; etc.) These examples disrespect the intelligence of the audience rather than overestimate it.
To put things this way: Which explanation of the Force do you prefer? A New Hope, Empire, or Phantom Menace?
To put things another way: No one would ever complain about Yoda's sublime description of the Force in Empire, but very many people complain about Qui-Gon's explanation to Anakin. There is a definite reason why.
Of course, that's forgetting that Darth Vader redeemed himself, killed the Emperor and returned to Anakin Skywalker when Luke lifted his helmet. This naturally led to the poignant scene at the end of ROTJ where the newly-redeemed Anakin takes his rightful place with the other Jedi.
This recent change is illogical, lame, and obviously done so that the crappy Lucas Prequels can insert even more control over the superior OT. Lucas continually tries to get the Prequel scenes and story into the OT, like some ugly guy hanging out with a pretty boy, hoping some of the charm will rub off.
4.) Shorten the podrace sequence, specifically by removing the pre-race introductions, the awful broadcasters, and Jar-Jar's cheering and by not having Anakin's podracer stall out at the beginning of the race. I cringe every time I watch the beginning of the Podrace. The final lap is decent and is all that was required to make the race seem dramatic and dangerous. The first two laps remove the tension. I also think Jabba should be more menacing in this scene, perhaps by having him laugh every time a racer dies.
5.) I am not a pure Jar-Jar hater like most peopl