(Keep in mind what I'm writing is an extremely skeletal overview, they would need to add more action scenes, ect)

Episode 1 should have started with Obiwan (as an actual Jedi) chasing a high profile enemy through space, they wind up in Tatooine where Anakin is a (get this) fucking pilot (a crucial part of his character in the later trilogy that was never even touched on in the prequels) working as air defence as a slave. He winds up being in the air space that Obiwan and the bad guy are flying through. Obiwan can't seem to be able to hit the enemy ship, but Anakin winds up using superior moves in an inferior ship and disables the enemy craft. Anakin and Obiwan share some dialog and Obiwan feels a strong presence in the force. He makes Anakin try a few easy force skills which Anakin fails miserably at and Obiwan decides to move on. Then out of the blue Anakin mind tricks someone (a higher jedi skill) without having to wave his hand showing an increadible ability to use the force. Obiwan (who could through the course of the first film) could set up that it is time for him to take an apprentice. The councel would feel weary as they sense danger in the boy, but would trust Obiwan due to his service and being a seasoned jedi.

Episode 2 should have been his training as a jedi, and pilot in the military with Obiwan, he could be assigned as a royal airman protecting the queen. She gets kidnapped, they have to board a star destroyer (or whatever variation of it was around before the Empire) save her and starting the relationship with Padme. Through this movie they also need ot establish Anakin as a leader, maybe having Obiwan be injured and having Anakin be the squadron leader. This would concrete Obiwan's personality traits as a sage, and having Anakin start leading people in a very cold and calculated way. The could also establish Padme was in on being kidnapped and she was really trying to escape her home planet and join the empire. She would introduce Anakin to Palpatine in this, and Palpatine would show Anakin force powers that the jedi would never teach him. He could do this under the guise that it would be a more effective way to "protect" Padme.

Episode 3 should have been the counsel finding out about Padme and Anakins relationship, forbidding it, Palpatine's continued teachings to Anakin, Obiwan and Anakin fight, Darth Vader intro, Tie Fighter reveal (Vader Custom),  and disbanding of the Jedi counsel. (Yes, it would be a LOT to cover, but it's the explosive conclusion to the epic prequel trilogy!)

Oh, and reduce CGI as much as possible. Is it just me, or is the Chewbacca from 4-6 more realistic than the CGI one? In fact, anything made in CGI looks so much worse. Jabba. Everything. I'll take proper old-fashioned special effects over CGI any day.

Objectivity can be found in all things, even in the Entertainment media. Just because something is subjective, doesn't mean it can't have objective effects.

The machete order. 4,5,2,3,6
http://www.cinelinx.com/movie-stuff/item/5721-star-wars-the-machete-order.html

Too much hideous stuff like Jar-Jar, senseless stuff like Padmé letting herself die after giving birth, that just doesn't fit with her character, but essentially the prequels should have been written BEFORE the sequels, because the problem is with Lucas himself: just look at the manic, obsessive and pedantic work he constantly did changing bits in the original trilogy, getting old he lost just a little bit of creativity, but unfortunately he's become pedantic, and it shows in the trilogy prequel, he didn't have the best ideas for everything in it, but it could have been a lesser fault if he weren't so pedantic to try and make bad ideas fit at all costs in the whole story. If he let a few things untold, maybe he'd have made the minority of obsessive and pedantic fans unhappy, but' he'd have done a far better job.

Ask Mr. Plinkett: https://www.youtube.com/watch?v=FxKtZmQgxrI&list=PLF34EBB1D68064251

Episode I Alone:

- Federation (Bad Guys) Vs. Galactic Republic (Good Guys)

- Anakin is 14-years-old to start the film, not 9. He's a slave who races in pod races controlled by local crime bosses. He lives a very hard life, not knowing where his next meal will come from, trying to scrounge enough to help his ill mother. He doesn't live in a cozy Flintstones hut. He's a good kid, he helps out other homeless slaves and tries to use his pod earnings to feed as many of them as possible. Poverty is rife on Tatooine. His mom dies leaving him orphaned, Obi-Wan feeling sorry for him agrees to take him to Coruscant and the Jedi temple at least. 

- As much as I like Qui-Gon, I think I'd axe his character or kill him off earlier in Phantom Menace. This forces Obi-Wan to become the lead character and creates an immediate narrative between Obi-Wan, Padme, and Anakin. The sooner we can get the story to focus on the relationship of these three, the more pay-off you'll have down the line.

- Darth Maul is a murdering bad ass and he is hell bent on killing the Queen. He kills one of her hand maidens very early in the film when. Also screw the "rule of two", he has several cyborg type "hunters" that operate with him. This way our heroes are the underdog from frame 1 creating something called drama.

- Naboo is under full siege and full invasion by the FEDERATION ARMY. All contact to the planet has been cut off. The first half of the film plays a bit like the Die Hard movies. Obi-Wan is a hot shot young new Jedi who was expecting an easy first major assignment, but everything goes to hell when the planet is taken under siege and he has to go underground and find a way into the Castle City of Naboo and he's badly outgunned by the bad guys. He does manage to get the Queen out, but barely.

- In keeping with the original story, they do manage to escape from Naboo but barely with Darth Maul hot on their tails. They crash land on Tatooine, and here Obi-Wan and Padme first meet Anakin. Obi-Wan is shocked by Anakin's inate ability to use the Force. 

- Obi-Wan notices something is wrong with the Federation troops, and voices his concerns to Palptaine and other politicians on Coruscant but no one listens. Queen Padme insist that he become her personal guard, the Jedi want him to watch over Anakin. The Senate declares a state of emergency.

- Anakin being a typical 14-year old in other ways, has a natural crush on the beautiful Queen, but she has feelings for the older, dashing Obi-Wan. Though she being a prim and proper monarch tries to keep these bubbling feelings down inside of her. Obi-Wan doesn't particularly care for royalty.

- The heroes go back to take on the Federation and retake Naboo, but the Republic Fleet is AMBUSHED by Federation Clones (Mandalorians!). What they thought would be a cake walk turns into a disaster as the Federation has far more troops and ships than they thought. The Republic (good guys) engage in a epic space battle, while the Queen and Obi-Wan head down to the surface, the ship Anakin is on is crippled, the pilot has been killed. Anakin is forced to take over the controls and reach out and lets the Force guide him.

- Not only does Anakin guide the ship and its crew out of danger, but he's able to deal a death blow to the Federation's main ship in the process. On the planet surface, Obi-Wan comes face to face with Darth Maul and they engage in a deadly one on one battle that leaves Darth Maul dead (?).

- The Republic (good guys) win but the losses are catastrophic. The film ends with a Senate scene where Palpatine seizes on the fears of the public to be granted the role of Chancellor and to create a Clone Army for the Republic to defend themselves against the Federation's own Clones. The good guys celebrate, but it's clear that a big war is brewing.

So at the end of Episode I, the Clone Wars are just at their beginning, which means Episode II can totally focus on the Clone Wars (rather than wasting another movie getting to that).

I thought they were great. People seem to forget star wars was made for children (teddy bear army in rotj that takes down a military force with technology of interstellar travel with sticks and rocks), just it was so well made we all grew up to it and loved it. Also people love to point out plot holes in the prequels but are happy to ignore that for instance in the time Han flys to bespin, Luke flys to dagobah and learns the basics of a jedi and enough skill to go up against a seasoned master and hold his own.

I love all six and watch them all the time and I love how the prequels go about with Anakin. Darth Plagueis had anakin as a force baby, darth sidious setting everyone up and making sure anakin hooked up with padme to set that wall up and with the end result of gaining anakin and becoming emperor.

I wouldnt make them. Direct prequal stories are always weak because you already know how its going to end. If we didnt, i'm sure they would have been movies much better received.

Erase Jar-Jar...Rewrite episode I to be less shit, more action and less bullshit and useless talk, explore Qui-Gon Jinn better, only killing him in episode 3.

Ya see, i would turn episode II in episode I, Re-introduce Anakin and Obiwan as fellow disciples of Qui-Gon Jinn, i would put ben/Anakin more like brother, than master and disciple, alson i'd put Dooku as the Villan from the start, i would use the "clone wars" side storys to make episode II and put lot's of Jedi deaths and show Obiwan and Anakin turning in jedi knights and introduce Grievous, and i would make Anakin be the one that kills Qui-Gon Jinn in a dramatic "father and son" like battle on episode III, followed by a battle whit obiwan...