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.) Midi-Chlorians. Most have read my opinions on the matter. I'm tired of this issue so I just left it out.
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 people. I do hate scenes like when the creature farts at him on Tatooine, and other cheap attempts at humor. I actually think the character had some potential, and not all of his scenes were bad, but many of them were. I actually think the dialogue between Jar-Jar and Padme on Coruscant is excellent, but Jar-Jar's actions in the Battle of Naboo do not like up to his promise of those key lines "Gungans get pasted too, eh? ... Wesa no dying without a fight. Wesa got grand army." I actually love these lines, but they emphasized a change and maturation in Jar-Jar that never came to be. Much like Anakin in the space battle, Jar-Jar is not heroic, he is a stupid coward who gets lucky. We should have seen Jar-Jar's character develop over the course of the film, from initially being a clumsy kid and then learning from the example set by the Jedi and becoming a proud Gungan warrior once the time of crisis puts his people in danger. Jar-Jar should have learned from the Jedi over the course of his travels (specifically, have Qui-Gon give him a peice of advice about fighting droids that he teaches the Gungans later on) and then come back a changed person. We should have seen him rescuing Captain Tarpals in the battle (not vice-versa), and then have him be named general, and make it a bittersweet occasion as he learns he is relieved of his life debt. It also would have been nice to have Jar-Jar demonstrate a fraction of the loyalty to Qui-Gon that Chewie shows towards Han with his life debt. Jar-Jar should have been visibly upset any time he was separated from Qui-Gon, to demonstrate his basic goodness underneath the clumsiness and immaturity, and done some sort of mourning at the funeral (like Chewie's at the Carbonite Chamber).
6.) At least a few Gungans should die in the Battle of Naboo (Hell, even an Ewok died in ROTJ). When Sidious says "Wipe them out, all of them," the droids should have obeyed this command. It actually bothers me when the droids start taking the Gungans prisoner. The droid control ship should go down during the heat of battle, not after the Gungan surrender.
7.) Either re-do the voices of the battle droids with a deeper voice, or have them use no voice at all. The destroyer droids were cooler and more menacing because they did not speak. The same could have been done for the battle droids.
8.) Another main problem I have with the Phantom Menace is the contrived plot device of the leaking hyperdrive. When the pilot rushes to deliver the line "the hyperdrive is leaking" just seconds after passing the blockade it feels very contrived, as does Obi-Wan's super quick reaction to the problem "Here, Tatooine". The hyperdrive problem was already done to death in Empire, and it should not have been used again. The writers could have found some other way for the characters to be stranded on Tatooine. It could have been as simple as saying that the Trade Federation would recognize their ship and destroy it at Coruscant, so that the characters need to buy a new ship. I think the hyperdrive problem is a glaring, sloppy error to the film.
9.) C-3P0 should not have been created by Anakin. His dialogue in TPM is also horrendous at times (ie- repeated lines: "That Jar-Jar creature is quite unusual"). C-3P0 would have worked better as a servant of the Naboo, or as a translator in the Senate, and R2-D2 would have worked better as Anakin's creation. He's the astrodroid with spunk and attitude, after all.
10) HAYDEN'S ACTING: Apart from his lack of tallent, Hayden's horrible portrayal was heightened to obviousness by two factors; bad scripting and bad directing. George Lucas has absolutely no idea how to write or play psychology. The character he created in a young Anakin Skywalker was comparible to a whiney 15-year-old pitching a fit when his father won't let him have the car for the weekend despite being underage as well as ignorant. There was nothing menacing, nothing intimidating, nothing remotely scary in the Anakin he was before Darth Vader. There's not even a shadow of Darth Vader in him. Darth Vader's hatred, all of his anger, would have to have been completely bottled up within him before he became the tyranical war leader. It would have been so subsided that even he didn't know it was there. He would struggle with it, but not know why. Then Darth Sideous, seeing the young man's tallent and potential, would draw that anger out of him and turn him toward the darkside. Recall how horrible Mark Hammil's acting was? However, it was overshadowed by good characterization. Hammil had a lot of anger he was dealing with in regards to an absent father. The character was just written better. Anakin's anger was more Freudian than that with the loss of his mother. However, no where has Anakin ever displayed the type of emotion worthy of being considered a leader. He makes poor childish decisions on a whim without thinking, lashing out without temprament. A leader must be wiser than that. Palpatine shouldn't have seen any potential in su