Some crazy ideas I had for the prequels, some radical, others not so much:
Maybe TPM's finale could be arranged around Anakin taking out the droid controlship. Qui-Gon is dead, Amidala is captured, and the Gungans are dying on the battlefield. After Qui-Gon's death, Anakin hears his voice, like Luke heard Obi-Wan's voice during the Death Star battle. The line "Remember, feel don't think" could be re-used. Anakin pilots (not by accident) his ship into the droid controlship, and takes it out. This way, Anakin is the true hero of the Battle of Naboo, and we also see just how strong he is with the Force. It could also be a nice mirror of the earlier mentioned scene in ANH.
Another idea I had was having Qui-Gon's body disappear, after he dies. The explanation Jedi disappearing as given in ROTS felt forced, and never made much sense to me. If it's something a Jedi has to learn, how did Anakin manage to reappear as a ghost?
I have no trouble believing that a Jedi disappering after his death has something to do with his state of mind. Obi-Wan sacrificed himself, Yoda went prepared and peaceful to his death, as did Darth Vader. The same could be said for Qui-Gon. Jedi like Mace Windu and the Jedi who died in battle didn't disappear, because they couldn't "prepare" for the deaths.
Having Qui-Gon's body disappear would sidestep the problem of having a forced explanation in the final 5 minutes of ROTS.
An idea I had for for the Senate scenes in AOTC was to remove some of the lights of the Senate pods lined up against the wall. The crawl states that many systems have left the Republic, so the pods of the senators of those systems would be unused, and there wouldn't be any need to see those pods "activated". I think it would be a subtle way of showing just how much the Republic is falling apart, especially in contrast with TPM.