Am still bummed that they killed off two good characters halfway through the first movie. Qui-Gon woulda' made a great 'loose-canon' cop type of figure, that could have shown Anakin an alternative to the monkish, "stand back and watch" Jedi council. Anakin could have been the young guy who, following what he see's an older guy do, goes to far and then begins the slide to dark side.
And Darth Maul was the sickest villain since Vader. What a shame. Lucas really needed an story editor who could stand up to him.
Sorry, these ideas suck. Qui-gon _needed_ to die. With him dead, there was no-one left among the Jedi who trusted Anakin. His own master didn't trust him until the beginning of Ep3, and Mace Windu took even longer. Yoda _never_ trusted him. If Anakin had a true advocate throughout the prequels, how the hell do you think he'd be so sweet-talked into buddying up with Palpatine? Palpatine used the jedi's distrust of Anakin to open up "another way" that he could follow. Qui-gon's "rebelliousness" towards the Jedi Council showed that there was weakness in the system. A Sith Lord moved in right under their literal noses. Dooku shows this rebellious streak, but corrupted.
Maul being a returning antagonist? Please! Maul's purpose to the narrative was to be the first sign of a resurgent Sith. He was little more than a disposable pit-bull to Palpatine. Do you honestly think Maul could've been the "face" of the Confederacy like Count Dooku was? Of course not. Sith Apprentices are, by nature, disposable.