Anakin was an annoying kid in ep 1, a shitty brat teenager in ep 2 and a decent human being in ep 3...story of Anakins downfall was straight forwardwas good enough but Hayden didn't ever come across as heroic when he needed to be in ep 3; that was the biggest strike against him tbh. If you watch TCW and ROTS, its as if they are two different Anakins. The cartoon version was much more believable of a hero with a dark side to him. Had he been like that in ROTS we could have gotten behind him a little more.
If youre really looking at the story; scrap the one apprentice plot point for the Sith and Jedi; have Qui Gon teaching both Obi Wan and Anakin in ep 1; develop a tight friendship between Padme, Anakin and Obi Wan hinting at a slight love triangle between the three in ep 2, have Dooku and Maul apprentice under Sidious at the same time, keep Maul alive until he's fed to Anakin in ep 3....