I did something similair over on Yakface, but I said what would you change in the movies and listed all of them 1 through 6, these are the changes I would make to the movies.
Ok things I would change.
Here are some ideas:
1) Change Naboo to Alderaan - it would make the whole story make more sense, and it would make Alderaan an important target again, but this time for the Trade Federation.
2) Introduce Bail Organa and Owen Lars at this movie -- these are the people who brought Luke and Leia up, they're important, I would do a homage and make Owen and Beru know Anakin Skywalker - ALA A New Hope cut scene with Biggs and Cami and Fixer.
3) Make Anakin a little older (and a better actor) and give him a personality
4) Keep Jar-Jar as is but make him less of a bumbling fool, similair to the new Clone Wars.
5) I would have C-3PO and R2-D2 as part of the Alderaan Royal Court, so they would be together from day one.
6) I would make Obi-Wan the Jedi Master and Qui-Gon Jinn the Apprentice, and then Obi-Wan could have been taught by Yoda, and then he looses the Qui-Gon Jinn Padawan to Darth Maul, and Starts to Train Anakin as his new Padawan.
7) Darth Maul should have been used more, and kept around till the second movie, and have dooku be his apprentice.
Change the Pod Race and get rid of all the CGI Aliens, and use Aliens Already Established from the WEG RPG Books (this means using established alien species long before the PT Aliens appeared on screen), in other words make it better and similair to the Races in the Droids Cartoon, hell even use Thall Joben and Jord Dusat.
9) Anakin should not save the day here, it should have been Obi-Wan and the forces of Alderaan.
10) No midi-chlorins more mysticism
11) No virgin birth, however keep Mysterious Birth (to latter be explained away or not)
12) Make Breha Organa the Queen of Alderaan, with Princess Padme Organa as her younger Sister and show both in this movie.
1) More development and back story of Obi-Wan
2) Better back story for Boba Fett
3) More about the Jedi and the way they train and work
4) Better Actor to portray Anakin - Hayden cant act
5) Have the death of Anakin's mother as the first scene of the movie, thus making it significant to Anakin's state of mind throughout the next 2 movies.
Possible idea: Obi-Wan wishes to negotiate with the Sandpeople. Anakin goes against this idea and attempts a failed rescue. Anakin blames himself and Obi-Wan and the Jedi for not being able to do anymore and not acting quicker. Palpatine gloats over Jedi indifference to family, and starts to use this to sway Anakin over to his side, by stating if he had only known he would have intervined. This would give Anakin's decision to switch sides more grounding, this would come from the fact his mother had died and the way the jedi handle emotions.
1) Anakin should not walk away when he finds out who Palpatine is because by this time Palpatine should have been able to seduce Anakin with the promise or power and greatness, but keep reminding Anakin that the Jedi would not allow this (basically letting the dark side take control off Anakin)
2) Obi-Wan should not be responsible for leaving Anakin to burn and die, this isnt in his character, hell they were considered to be brothers - would you walk away and leave your brother to die.
3) More about the Fledgeling Rebellion and Padme's role as one of its co-founders.
4) A more respectable death to Padme, and a more heroic one.
5) More screen time for Vader in suit - I would have the scene where Obi-Wan and him Fight earlier on and have Obi-Wan try to bring him back over to the light side, believing its not to late, like he tells Luke "I once thought like you but hes more machine than man now" or something along those lines.
Remove all re-release additions to the movie except cool scenery, and some of the more interesting Aliens.