If I had my druthers, I'd change the entire approach to the Star Wars prequels. Most of the basic material would remain, but the following constitute major changes.
Star Wars Episode I: The Phantom Menace: Anakin is still a slave, and Padme Amidala is still a queen; Qui-Gon is still a Jedi Master and Obi-Wan is still his padawan. However, the tone of the film would change. I would have severely cut the entire pod-race scene, I would have added more scenes of Anakin having anger-issues and being somewhat of a prickly, although very intelligent and force-touched, child. There would have been an explanation as to why the Trade Federation's blockade was reduced, and I would have given a better explanation for why the Jedi Council didn't want to make Anakin a Jedi, focusing on the fact that they've become complacent in their power and status, a reflection of one of the reasons why there is a need for a realignment of the Force. And there would not have been Jar-Jar Binks, C3P0 or R2D2; some new droids are in order or no droids at all. Finally, I would have introduced a very young Wilhuff Tarkin as one of the pilots that helps Amidala escape and return to Naboo.
Star Wars Episode II: Attack of the Clones: Amidala is deposed as the Queen of Naboo due to rising tensions in the Republic that have affected her world's economy. She believes, through her own spies, that part of the upheaval is due to the machinations of a powerful merchant, a former Jedi Knight named Count Dooku. She is ferreted out of Naboo safefly by Bail Organa (a former colleauge of her father or something), with whom she begins a relationship. Despite Senator Organa's support, the Chancellor, Palpatine does not feel it would appropriate for him to provide direct aid to Padme and so he sends her former friends, Obi-Wan and Anakin to help ferret out the situation. The Chancellor also gives them a military attache, Tarkin, to help out. While Tarkin and Anakin get along quite well, this arrangement does not please Kenobi nor the Jedi Council and this is where we begin to see the stirrings of issues between the Jedi and Palpetine. Anakin is not in love with Padme nor she with him; rather, he comes to depend upon her as he learns about and deals with his mother, his place in the Jedi Order, and his challenges with Obi-Wan, who has no idea how to deal with the far more powerful, yet under-experienced padawan. Padme, who was never married, comes to find it appealing helping the younger Anakin. Obi-Wan is still captured by Count Dooku and Anakin still defies both his master and the Jedi Council to rescue him; he and Padme are captured as well and that's when they realize they're in love. The Jedi Knights, with aid from Tarkin and his troops, arrive in time to start the Clone Wars and save the trio. The same conclusion, except that Padme and Anakin aren't married at all; rather, this begins a series of one-night stands despite her marriage to Organa. The theme here would be to reflect how Anakin is in the middle of a bubbling conflict between political powers represented by Kenobi (who's aware of the limitations of the Jedi that are in power and feels impotent to address it) and Tarkin (who represents the growing power of the Executive Branch of the Republic). In other words, there were problems brewing all the while; they didn't just suddenly appear in the next film. Finally, we introduce General Grievous here.
Star Wars Episode III: Revenge of the Sith: Obi-Wan is a Jedi Master and Anakin is a Jedi Knight. They still have more of a father/son relationship that is struggling to develop into something else, but they don't partner together and Obi-Wan has a new padawan who dies early on at the hands of General Grievous. Anakin and Tarkin are very good friends and Tarkin works directly for the Chancellor. Padme accidentally becomes pregnant by Anakin as the two are still having an affair, one of which Organa -- who's very much in love with Padme -- knows about it and tries tostop it. Anakin, still has dreams, still thinks about his mother, and wants Padme for himself, is furious when she calls the affair off. Alongside the issues with the war and the Jedi, Anakin is seduced by the Darth Sidious to the Dark Side. The final fight between Anakin, now Darth Vader, and Kenobi begins with Kenobi stopping Vader from killing Padme (there's no grand, insipid speech). Vader is winning all the while, but his inexperience and ego cause him fall to a simple trick Kenobi pulls which results in his dismemberment and immolation. Padme survives a broken woman after having her twins; during labor, she passes out and Kenobi and Yoda take Luke, while they let her keep Leia. A good man, Organa promises to raise her as his own despite knowing he's not the father and Padme leaves, a broken, bitter woman. After he dons the suit, Vader doesn't do a Frankenstein "NOOOO!" He screams. The end. The point here is that the entire overwhelming situation, his thirst for power, his anger, and his desire to control everything around him leads to Anakin's downfall into Darth Vader.
Finally, Lucas doesn't direct any of these movies. The inclusion of Tarkin is to draw parallels between the relationship between Luke and Han Solo.