When I saw the trailers and some of the leaked production photos from TPM my speculations of what would happen were very different to the final film.
The Trade Federation Tank prop was shown at the studio with some Tatooine looking items in one photograph I saw which lead me to believe that the Trade Federation Battledroids would invade Tatooine at some point, which would justify the anti-droid sentiment shown in ANH.
The Magnoliafan take on the Federation (that they were dealing in slavery) would tie in with Anakin's slave background too.
Perhaps by recolouring some scenes from AOTC it might be possible to create a crisis on Tatooine which would create a more dramatic origin story for Anakin.
The Geonosians are seen in AOTC as being fond of Gladitorial combat, which could extend to Pod Racing.
So one possible huge re-jig would be to put the Trade Federation primarily into the hands of the Geonosians instead of the Neimodians (who could be just a lesser member race).
This would return to the original intent of the battle droids being built to resemble their masters.
I also assumed that the lightsabre duel between Maul, Qui-Gon and Obi Wan was taking place on a star ship.
It might be possible to alter the scenes at the beginning of the film as seen and cutting into the duel (with adjustments) so that the Jedi encounter the Sith Lord on the Trade Federation ship.
I also assumed that all the Naboo hanger scenes would happen at the same time (surely the Trade Federation would have destroyed or disabled the Naboo fighters rather than just leave them hanging there to be launched against them at the end of the film).
So one possible alteration would be to start the film on Coruscant with Queen Amidala protesting about the blockade of her planet. She goes (with a Jedi escort and the Gungan Ambassador Jar-Jar) to effect a liberation of her planet but is hijacked on route and forced to land on Tatooine which has already fallen to the Federation. They meet up with Anakin, gain the parts they need, Anakin joins the Jedi hoping to liberate Tatooine at a later date (giving Anakin a noble intention for leaving his mother behind rather than just seeing the stars).
As they escape they encounter a Sith Lord who is working with the Federation (I'd love to be able to put the Obi-Wan vs Maul scene that only happened in this publicity photo but I haven't a clue how).
I find it hard to believe that they flew Ewan over to Tunisia just to film a few shots outside Amidala's ship.
They break through the blockade and create a hasty alliance with the Gungans. The Gungan's attack the bulk of the droid army, The Jedi attempt to shut down the shields for Trade Federation command ship and encounter battle droids (which should rarely if ever speak and certainly should not be the comic relief goons as seen in the theatrical version...incidently they do sound good in German) and finally the Sith Lord they first encountered on Tatooine, the Naboo fighters clear the path for the Jedi and take on the full Federation fleet (not just one ship making it an more hopless fight) and the Queen and her troops storm the palace.
Jar-Jar would have a less prominant role and would be dubbed to turn him in a dignified but quixotic ambassador.
Anakin's dreams of liberating the slaves on Tatooine would come true with a tragic twist in the next film as Geonosis is now Tatooine the site of the first big battle of the Clone Wars.
The Federation fleet would retreat once it's command ship is lost leaving their Neimodian lackys to take the blame.
The scene with Dooku forming the Seperatists would be moved to a meeting on Tatooine placing Dooku into the first film and making it seem as he is the prime Sith Lord.
I'd remove all Sidious scenes from the first film and have him make his first appearence in the second film.
I'd also remove or alter all the joke alien pod racers and have them all gladiator slaves of the Federation.
As in most re-edits Jake Lloyd's performances would need to be toned down to make him less annoying and the Jedi Temple scenes would be placed at the end of the film (minus Qui Gon) with Obi-wan being reluctantly being allowed to school Anakin because of his obvious nascent Jedi abilities (not because of the dreaded midichlorians).
I'd also would like Darth Maul speak more by sampling some dialogue from the PSone game (where I believe he has more to say) and the Eulogy To Fear (no not the one in Dune) heard in the trailer which (as in the trailer) balances Yoda's warning about fear leading to the Dark Side.
When the student is ready, the Master speaks?