I first decided to write up my own version of the PT years ago, back in 2008. My original plan was to take the George Lucas scripts and simply touch them up - leave most of the actual storyline, characters, dialogue, scenes, etc. intact, but change some of the details so they would line up more with how I thought the PT should have unfolded (older Anakin, Yoda as Obi-Wan's master, clones as the enemy, stuff like that).
The decision was made to take AOTC - the prequel I thought was the worst and need the most rewriting - fix it up, and then work my way backward to the TPM script, touch it up, then finish with ROTS. In the end, though, that plan fizzled out; I did rewrite AOTC, but eventually tossed it out, never finishing the touch up on TPM or getting to ROTS. When I decided to start again on my alternate PT, I went with the classic linear approach - first prequel first, second prequel second, etc, etc. Instead of just touching up the Lucas scripts, I would scrap them almost totally, using only some of the plot ideas and scenes as a framework of sorts - a bare foundation to build upon.
But though the "Touched Up PT Edition" never made it off the ground, I did write down some ideas on how it would all unfold; here are the "touch ups" I conceived for TPM.
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The Clone Wars begin shortly before the first episode of the trilogy. Again, the conflict begins with inner turmoil affecting the Republic, with several dissatisfied planets seeking to separate and establish their own independant confederacy. The war causes peaceful trading relations between the Neimoidians and the people of Naboo to dissolve. The Trade Federation blockades Naboo, ultimately leading to a plan to invade the world and take direct control of its resources.
Obi-Wan is older, thirty years old, a Jedi Knight who was trained by Jedi Master Yoda. He is the only ambassador sent to Naboo; Qui-Gon is not with him. Ultimately he's the one who discovers Anakin on Tatooine and decides to take the boy on as his Padawan.
Qui-Gon is no longer the Master who trained Obi-Wan. Instead he is a friend of Obi-Wan, almost a father figure. His role is reduced; he does not journey with Obi-Wan to Naboo or Tatooine. He weilds a blue-green lightsaber instead of a green one.
Owen Lars is introduced. He is the half-brother of Anakin, born two years before him. He lived with Shmi and Anakin his whole life. He unsuccessfully attempted to change Anakin's mind when the boy chose to leave Tatooine to train under Obi-Wan, leading to a life-long grudge towards the Jedi Knight.
Palpatine (in his Darth Sidious persona) is never the shadowy Sith Lord working behind the scenes to sow discord within the Republic. Darth Maul fills that role, working as Palpatine's figurehead.
Darth Maul's role is expanded. He is the one who communicates with the Separatists and guides their actions (under Palpatine's orders). The end duel between Darth Maul and Obi-Wan ends with the Jedi slashing him through the shoulder instead through the torso. Maul survives and recovers to menace the Jedi again.
Anakin is twenty when Obi-Wan discovers him. He is not conceived by midi-chlorians and isn't "born from a virgin"; his father was an unknown Force-sensitive man who had a brief relationship with Shmi before he mysteriously disappeared.
The Gungans do not possess a thick Jamaican accent, and speak nearly average Basic.
Jar Jar Binks has a child-like personality, but he is also brave and not a bumbling buffoon.
The Podrace is replaced with a skyhopper race.
A mutual attraction between Anakin and Padmé is established almost instantly upon their introduction to one another. By the end of the first prequel, a tenuous romance is formed between them.
The Jedi are much like the Jedi in George's PT, and their opinion of and reaction towards Anakin is the same.