I wouldn't have killed Darth Maul. I would have had him escape at the end of episode 1. I wouldn't have made Count Dooku a Sith either. I just can't see him being an "apprentice" to anybody if he was as powerful as they made him out to be. I think he should have just been a separatist Jedi who didn't agree with the republic. Maybe the Jedi order his assassination or something and it doesn't sit well with Anakin or some shit. He learns stuff from Dooku or whatever, but refuses to leave the order because he still believes they are good and he believes in his mentor Obi. Then Obi receives information that Maul has been found, disobeys orders and takes Anakin to pursue him. Anakin gets hurt, Obi kills Maul. Anakin sees that the Jedi order isn't the pure order it was supposed to be yada yada yada. Somewhere in there, him and Padme get it on, his mom dies, fill in the rest.
"Everything we hear is an opinion, not a fact. Everything we see is a perspective, not the truth." -My good friend Mark Aurelius
