This is a list of all the major changes I would make to the current Prequel Trilogy:

The Clone War that is fought during the Trilogy should not be the only Clone War. Before the Prequels, there should be another Clone War, in which the Clone Masters created an Army of Clones and tried to take over the Galaxy, just like the Thrawn Trilogy says. Thus, the First Clone War is the one that was fought against the Clone Masters, while the Second Clone War is the one that was fought against the Separatists and it’s the one that was fought during the Prequel Trilogy, and in which Obi-Wan and Anakin participated. This way, the Clone Wars from the Thrawn Trilogy could be seen as true and there would be no significant contradiction with the pre-1999 EU, but at the same time we could also have a war against the Separatists.
Anakin’s discovery, his taking by Obi-Wan and how he joined the Jedi Order should be themes that stay out of the movies, they should be themes for novels and comics set before the Prequel Trilogy, between the two Clone Wars. In the first movie, Anakin should be portrayed as Obi-Wan’s apprentice already. The first movie should be like Attack of the Clones, that is, a movie that serves to establish the beginning of the war (the Second Clone War) and the beginning of Anakin and Padmé’s relationship: the second movie should be like Labyrinth of Evil, that Is, an adventure that is set during the War itself; the third movie should be like the classical Revenge of the Sith, so it should show Anakin’s fall and the birth of the Empire.
Anakin and Padmé should meet for the first time in the first movie. They doesn’t marry in the movie, nor for the rest of the Trilogy. Their relationship is not a marriage, but just a normal romantic relationship. Thus, Padmé is not Anakin’s wife, but simply his girlfriend. Furthermore, Padmé should still be the Senator of Naboo, but she should not be the former Queen. Jamilia should be the Queen all along. So, Anakin and Padmé meet each other when he’s 20 and she’s 25.
There should be no rule forbidding the Jedi from having attachments, and the Jedi should be free to have romantic relationships. In general, the Jedi from the Prequel Trilogy should be more like the Jedi from the Tales of the Jedi comics. They should be heroes and should value positive feelings and positive relationships. Instead of teaching how to avoid relationships, the Jedi should teach how to have good relationships and should allow falling in love. Thus, Anakin and Padmé’s relationship should be public, and attachment management shouldn’t be the main storyline of the Trilogy, nor the reason of why Anakin falls to the Dark Side. I have nothing against the idea that the Jedi have their vision clouded by the Dark Side, and I’m also not against the idea that they have become a bureaucratized institution that puts itself at the service of corrupt politicians. I mean, I don’t want the Jedi to be portrayed as perfect through the Trilogy, but at the same time I’d like the audience to be able to share their basic philosophy, and I also don’t want them to forbid such a natural thing as falling in love.
Anakin doesn’t fall to the Dark Side to try to save Padmé, but simply to try to end the War. Yes, he’s a slightly rebellious and a little stubborn person, but at the same time he’s very peaceful and would not hurt anyone. In spite of this, the War eventually transform and radicalize him. Such a radicalization leeds Anakin to embrace authoritarian ideals as time goes by (he never treats Padmé badly, though). In the end, Anakin ends up getting so sick of all the War and all the suffering that he sees through the Galaxy on a daily bases, that he becomes willing to do anything to put an end to all of it. So, Palpatine reveals himself as the Dark Lord of the Sith who was always behind everything and offers Anakin to join him, to bring order to the Galaxy and stop the War. Anakin eventually accepts, but at the same time he becomes corrupted by the Darkness, to the point that he ends up doing things he never thought he would do, such as killing all the Jedi inside the Temple after the activation of Order 66. Then, he ends up killing Padmé (she dies in childbirth due to the injuries he gave her), and the duel on Mustafar would be the same, so he ends up being burned in lava.
I have nothing against the use of the Clones by the Republic, but I think the Separatists should use a Clone Army as well. So, Dooku and Palpatine would orchestrate the creation of the Grand Army of the Republic, but at the same time they would also create a Clone Army for the Confederacy, obviously using two different people to create the Clones. Also, Jango Fett should not exist. The Prequel Trilogy should respect the pre-1999 lore, therefore Boba Fett’s backstory shouldn’t change. So, the Clones used by the Republic are Clones of an important Mandalorian bounty hunter, which is not related to Boba Fett, though.
I have nothing against the idea of Yoda using a lightsaber to fight, but I think he should only use the lightsaber once, that is, during the final duel against Darth Sidious in the third movie. That should be the first and last time we see Yoda using his lightsaber in all of the movies.
Anakin is not the Chosen One. There should be no Chosen One in general. Anakin should have a biological father and mother like all normal humans, and he should be a normal human without any divine or special connotations. However, Anakin never knew his father, as he died before he was born. After Anakin left Tatooine to become a Jedi, Shmi married again. She married Cliegg Lars and lived with him, Owen and Beru for many years. However, she died before the Prequel Trilogy began, so we never see her. Sometimes Anakin mentions her during the course of the three movies, though, and throughout the trilogy Anakin should visit the Lars family at least once. This way, we have the opportunity to explore the frictions and differences between Owen and Anakin, of which Obi-Wan talks about in Star Wars (1977).

I’m currently planning to rewrite the Prequels by using this main concepts. My Trilogy will be based on the premise that most of the pre-1999 EU is Canon, and Rogue One will be considered Canon as well. If any of you are interested, maybe I could open a specific thread about it…