Anti-matter
I also thought that with some clever editing the gungans can be cut out all together. When Amidala decides to go back to Naboo instead of her asking for the gungans for help you can just cut to the part when she explains her plan to enter the palace thru the secret passage on the waterfall side. Her main goal can be to simply capture the Viceroy while the only battle that takes place is the space battle at the Fed. ship while the Jedi deal with Maul and her team enter the palace. Simply cut out all the gungan stuff and delete all references to the gungans. I saw TPM the other day and it can be possible.
I also had this idea as well, I was thinking if instead of having to see any of those excruciating "intimate scenes" between Padme and Anakin, why not simply make it look as they are already involved by the time Anakin is a young man? What i mean is, after the PTM section of the Prologue is over go back to tatoine and show Anakin as a boy and simply use a "fade" transition on tatoine and fade to him as a young man. That way there is no need for anymore text on the screen to denote the passage of time. You can fade to the time him and Padme are on tatoine perhaps at the Lars' homested looking for Shmi. Remove all the "My Jedi protector" nonsense and all the crap scenes between them on Naboo and just make it look like they are already involved and have been for years during the time after the liberation of naboo in TPM. Maybe even with some clever editing make it look like Anakin was living with the Lars all along... this compliments your idea of leaving boy Anakin on Tatoine. Then at the end of AOTC section, they marry. The only kissing scene that should even stay should be the one on Geonosis cutting out "...been dying a little bit each day since I saw you" *cringe* of course.