I thought about it for some time, if I was there as Lukas assistant, what would I try to improve? Surprisingly, in prequel trilogy not that much.
Only Midi-chlorian. Instead of symbiotic organism that channel force, I would go with that force sensitive people are excellent breeding ground for them and their symbiotic nature increases the strength of certain tissues, accelerates regeneration, and so on.
I would highly change Anakin, but not his inner darkness, but more how whiney he is. I would go with something like this to reveal the character:
Anakin: It's not so different, to be Jedi, than be a slave.
Padme: How can you say it!?
Anakin: Don't get me wrong, Jedi are kind masters. But I'm still not free. With Watto I couldn't leave, I couldn't have anything, I couldn't disobey. But with Jedi I have new forbiddance. I can't be angry, or sad... or love. Watto forbid me to do many things, but at least I could feel whatever I wanted. Gardulla would whip me as punishment, Jedi would send me meditate for hours and hours. Sometimes I would prefer a whip.
Padme: Oh, Ani. You know that you could leave Order, Naboo would gladly accept you as their hero.
Anakin: I don't think I want to. There are downsides, but I like being a Jedi. I learn so much. And I do something really good for the galaxy. But One Day, I will grow strong and wise. I will stop being some dangerous slave boy for the council. I will make them proud of me and see me as their equal.
Now we have ground to bitterness about not being a Jedi master, Anakin thinks that Council will never see him as equal + need to access to Jedi archives. After Anakin talks to Palpatine he is always dizzy, because of course Palpatine slowly poison his mind with Dark Side. Canonically Palpatine holds some influence on his mind, Anakin never said to him about his marriage or visions, but Palpatine knows about it. It's not control like Jedi mind tricks, more like extreme persuasiveness. He plants (with force help) ideas in his head for months and years.
When Anakin rush to Palpatine to save him, he had no chance to see Jedi body's. In his mind, Palpatine is part of ancient order, but that is totally legal. Jedi learns about that and wants to kill him like criminal, which he is not. It's not illegal to be Dark Sider. He was legitimate Chancellor that was doing a good work. Not responsible for Dooku, war and assassination attempt.
He still choke Padme on Mustafar, but when she collapse, he, for a second holds body so it won't hit the ground. In his mind, he simply puts her out of commission, so Padme wouldn't stand between him and Obi-Wan, because that is what padme would do, try to stop them from killing each other.
During the duel, instead of High ground moment, at some point, Obi-Wan disarm Anakin. He tries to Force Pull his Lightsaber. It's vibrating, but not moving, and than it's fly with easy, but not to Anakin, but to Obi-Wan, because this lightsaber was a weapon of the Jedi, not a Sith.
And in the end, when Vader ask about Padme
Sidious: I'm afraid that you killed her.
Vader: No, you lie. I feeled her heartbeat
Sidious: Oh, but you did. You see, I couldn't just let my true apprentice, one so powerful to simply die. I had to put life back in your body. But why would I give my own? Bond that you had with Padme was strong, dictated by Force itself, but Jedi would never allow it. So I used yours bond to channel life force of your wife to you.
Vader tries to attack Palpatine, but without success, because of new prothesis. Palpatine sends Force Lightning in Vader, he tries to block it, but Lightning hits prothesis.
Palpatine: you can't kill me, Vader. You think learner like you stand a chance against a master of Dark Side? No! You can't beat me, and, thanks to Kenobi, you never will. I designed this Life Support with that in mind.
Vader: I will kill you!!!
Sidious: you are not powerful enough. And, thanks to you, I am the only person left, who can teach you the power you need to kill me! Now. KNEEL!!!
Than with Obi-Wan and Yoda, they talk about how twins are only hope, because only they could kill Vader, as he subconsciously would feel how they are his children and will hold back.
Slight change when Ben find R2
Ben: I don't remember even owing you, little guy.
This is simply for my taste. When Tarkin commands to destroy Alderaan, Vader dramatically enters and says "No."
Tarkin: this is not for you to decide, I am commander of this station. Open fire!
Vader: I told you Moff, power of this station is insignificant compared to the power of the force.
And Vader turn the whole death star so it would miss Alderaan, but will get close to Millennium Falcon. Tarkin tries to accuse of treason, and Vader simply Force Choke him and Troopers who are stupid enough to aim at Vader. Leia almost crying out of relief, but Vader escorts her to her cell and says, that they still held her prisoner as terrorist.
Later, with Emperor, Tarkin tries to accuse Vader of treason, again, but Vader says, that destroying Alderaan would be stupid move. More people would go to the rebellion. Empire rules using fear, but they should fear to go against an Empire, not simply afraid that Empire would kill them without reason in random moment.
During escape, Leia is badass. At one moment when Leia grabs Han's blaster scene changes on her faces, Force music is playing and Leia hit all Troopers in heads. Han is amazed and notes, that blasters don't have that accuracy.
When Ben fights with Vader and Ben calls Vader the master of evil, Vader repeat his line, that good and evil depends on point of view, and from his point Jedi are evil. I would improve the fighting scene, there is one in YouTube.
On Yavin, Luke meets Rex, who enthusiastically tells about clone wars Days with Anakin. How his Dad treated clones as people, as brothers, instead of consumable people or meat droids, which not every Jedi did. How always personally led 501th in battle and for the best of his abilities tried to keep everyone alive.
At the start, add scene when Luke trains with lightsaber watching Holo-vid of Anakin and Ahsoka, trying to imitate their moves. (Yes, he got it from Ahsoka, but behind the scenes)
In Cloud City, when Han confront Vader... It's just badly directed, how Han's blaster flys to Vader is horrible. More intimidation, guys!
During duel of Luke and Vader, Luke strike Vader with that move, that Luke repeat from Holo-vid. Vader Don't cut Luke's arm, moves to do it is made, but Vader turns off saber in moment, and hits back of Luke's head with handle.
Emperor catches Han and Leia from Jabba and brings them to Death Star II. Luke learns about where they are and unites the remnants of resistance, which is not much. Luke meets his Father and they talk, but Vader is not going to bring Luke to Emperor. He does not 'must obey his master'. Instead, Vader says about how he was never good Jedi, too passionate, too impatient. How he does not believe in inner peace anymore, and brings sith's code in very passionate manner.
Peace is a lie. There is only Passion.
Through Passion, I gain Strength.
Through Strength, I gain Power.
Through Power, I gain Victory.
Through Victory my chains are Broken.
Luke: You don't look free.
And Vader honestly can't answer to that anything.
Vader wants to kill Emperor and get control of the empire. But Vader needs Luke's help, cause he can't resist Emperor's force lightning. Luke agreed to go against the Emperor, but he must turn off the protection field first.
Luke and Vader separate, so Luke could neutralize Field, and Vader goes to the Emperor as distraction. In that moment, Emperor brings to his throne room Han and Leia. Palpatine feels Leia' s force potential and says to Vader, that he did DNA taste, and that Leia, apparently, his daughter. Vader is shocked, that Padme had Twins. And Emperor says that it's reason to celebrate, but Father and Daughter shouldn't be be on opposite sides. So he fires Force Lightning in Leia, to torture her and make her turn to Dark Side. It's working, and on Leia fingers start dancing lightning. In this moment show conflict in Vader, to let daughter be tortured, to bring on his side against Palpatine (Emperor is sure that she will be on his side, since he is master, thus more powerful, end if not, than he can defeat both Vader and Leia and torture them in submission) or stop Palpatine, obsessive love against compassion. Vader decided to save Leia and attacks Palpatine, but it's not successful. One hand fires lightning on each Skywalker. "FOOL, you though you cold stop Me?" "He is not alone" Luke comes to throne room, Emperor change target from Leia to Luke, but he blocks it with lightsaber and redirect to guard that holds Han. Emperor sends lightning from both hands to Luke, not he still blocks it all. Vader looks between Emperor and Leia, and goes to Han, frees him from handicap, gives him Leia and orders to get her out of here. Luke and Vader united defeat Emperor, but Vader is seriously injured. Rebellion float being destroyed by death star (not finished, so no destroyed planets, but ships...) and empire forces. Skywalkers understand, that they need to help rebellion, Anakin says Luke to get out of Death Star, and that Anakin will reload reactor, to destroy the base. He is too injured (he would live, but now is barely on his feet) to escape after starting process. Luke wants to save Anakin, but he says that Luke already have and to let him do this, because Anakin wants to be his dad at least once, and father protects his children. Luke rush to angar, and Anakin starts self destruction of Death Star from console, that is in Throne Room. While he goes to it, he loose parts of his armor. After starting the process, he sends rebellion a message, under the name of General of the Republic Anakin Skywalker. He sends 3 separate messages, to Luke, to Leia and to 'Snips' with apologies for being a bad father and how proud he is. Than he looks at window, with sunset in space and war around, takes off his helmet, shows his blue eyes and mutters under his breath, "Well, Anakin. You were always good at killing people. Hope this time it's right ones." And collaps star destroyer on star destroyer, greatly reducing Empire's fleat. Out of overstrain of Force, Vader dies, his prothesis fall to the floor and he ascended to the force.
