1) I’d of jettisoned The Phantom Menace in its entirety; the first movie adds nothing to the story and is a convoluted, wasteful two hours better spent on a completely different and more interesting story idea. I’m of the mind that I could care less in seeing Anakin’s beginnings as a child, which is the entire point of the first film. Make Anakin a Jedi apprentice with a lot of potential and leave it at that; no talk of virgin births, prophecies, and midichlorians or any of that bull shit as it just doesn’t work and all comes across as silly.
Ultimately, my opinion of The Phantom Menace is that it doesn’t fit in with the rest of films and hampers the prequels with unnecessary exposition. The original trilogy had immediacy to every scene that pushed those films along and moved the overall three film story arc, something the prequels lack with this false start of a film. Deleting it takes care of certain characters and plot points that play no greater part or have little relevence in the other movies.
2) In getting rid of the first film and making a few script changes, I’d of made Attack of the Clones the first film in my prequel trilogy. Anakin is introduced in this first film as a Padawan learner to Obi-Wan Kenobi at basically the same age Luke is introduced in Star Wars and meets Padme for the first time near the beginning instead of being reunited with her. Otherwise, the film plays out close to how it actually does, except for my next point…
3) No marriage at the end of Clones; the whole romance in the second film is much too rushed and ham fisted. The entire Geonosis trip should play out as a playful first date of sorts for Anakin and Padme, not a prelude to nuptials or a declaration of undying love for one another.
4) The second film in my trilogy would take place during a pivotal time in The Clone Wars. With Clones we get to see the beginning of the war and with Revenge of the Sith the end, now we get a film that takes place during the conflict (and before you all yell "But what about the animated The Clone Wars?", I’ll state my opinion that if it didn’t happen in the films, as far as I am concerned, it didn’t happen). Something missing in the prequels is that we keep hearing about how Anakin is this great hero of the war and all, but it’s never seen on film and you never get a great sense of it. There is also room for the relationship between Obi-Wan and Anakin to become a deeper bond as there is a special comradery between soldiers that is born in times of war; you get a sense of it in Sith, but again you never see it develop so it loses some weight. Having a wartime picture also adds the potential to see the dark side in Anakin grow; as it stands his turn from good to evil in Revenge of the Sith feels like it takes about as much time as taking off a white hat and putting on a black one…a bit more build up would have been better.
5) Anakin and Padme would marry at the end of this new second film, having had time between the first two films to actually have a believable, evolving relationship before jumping headfirst into matrimony.
6) Count Dooku would return as the foreground villain in the film with Palpatine in the wings. Another missing component from the original trilogy is one bad guy who is consistent throughout the trilogy, such as Darth Vader. The prequel trilogy has a series of disposable bad guys running around, but no one who is a common thread to the films besides the shadowy and, to be quite honest, boring Darth Sidious. Count Dooku, as the elder statesman, fallen Jedi would fit this role perfectly in accordance to the structure of these films that are set in a more regal time period. And speaking of bad guys, General Grievous could have been this trilogy’s Boba Fett if handled differently (i.e. not as a cowardly joke) and introduced in this new, second film.
7) Revenge of the Sith would unfold pretty much as is, though I would have extended Count Dooku's part and swapped his place with General Grievous in the film. Just like Fett in Jedi, Grievous is there for the beginning but quickly dealt with.
8) I also would have kept the scene deleted from Sith where we see the Rebel Alliance born. It seems like too important of a scene to me to cast aside and would make a nice mirror image to the Rebel planning scene in Jedi.