So a few days ago, I left a comment on this article from Cracked.com about missing opportunities in fiction. The article mentioned, among other things, the Star Wars prequels and made a suggestion as to how they could be improved. Now like the entire population of the planet (and 30% of Mars) I too have had my own little "what if the prequels were good" fan fiction fantasy, and figured I'd take that opportunity to post it in a comment. Said comment has gotten some really great feedback, so I figured I'd re-post it here:
From where I stand, Anakin's fall to the Dark Side needed to mirror Luke's near-fall to the Dark Side in the original trilogy. The seeds of that arc are there (losing his hand, killing Dooku, etc), but there's no real focus on them and they carry no real weight. The Dooku death scene should have been at the end of Episode II or III to, and it needed to be treated with a lot more gravitas. The whole point of finale of Return of the Jedi was that if Luke killed Vader, that was it. Game over. He's on the Dark Side. No going back. Revenge of the Sith needed a similar scene where Anakin is tempted and, unlike Luke, gives in.
Personally, I'd have done it like this: first we relocate and expand on Darth Maul's role. He's already visually the most memorable thing in these films, so let's make make him an actual character rather than just a disposable hitman. He'd be the main villain of either the second or third film. He's cold, ruthless, and fanatically devoted to Palpatine. And he has one goal: to force Anakin to kill him. This was his mission given by Palpatine. He must pursue and hound Anakin, attack and kill his loved ones, assault everything he cares about, until Anakin's rage is so great that he takes his vengeance. He'd essentially be Legato from Trigun, a villain whose aim is to die just to torment his nemesis that much more.
So Maul appears in film 2 out of nowhere. He's deadly, mysterious, and no one in the Jedi Order can seem to stop him. He attacks the main characters one by one, killing one or more of them. Have a likable but dispensable supporting character set up from the first film for Maul to kill, someone that we can afford to lose but would mourn their death. Maul fights Obi-Wan to a stand still, and, in the final straw, tortures and nearly kills Padme with Force lightning. In a rage, Anakin engages him, barely in control, as Maul taunts him, daring him, even begging him to kill him. Perhaps this is the fight, where Anakin loses his hand. And at long last, Anakin cannot take it anymore and screaming in rage, kills Maul, who meets his death with a sadistic smile. He has won. Anakin's soul belongs to Palpatine now. He is a Sith.
That's his actual fall. The third film would be Anakin accepting his role as Vader. After all, a good man doesn't just flip a switch and become evil overnight. Perhaps he goes into self-imposed exile, haunted by what he did, wrestling with the blackness in his soul. He's eventually approached by Palpatine, who forces him to see the reality of what he has become. He has taken a life in anger and he can never come back from that. He is no longer a Jedi.
And from there it can more or less structurally play out like Revenge of the Sith. Anakin wipes out the Jedi, confronts Obi-Wan, they fight, Anakin get's burned, etc.
Hope you enjoyed that. And yes, I realize the irony in writing about this when I just recently berated my readers for not getting off the Prequel hate bandwagon, but hey, I never said the films weren't a missed opportunity.