Changes and Story Tweaks

PT Era

While the Jedi remain unchanged, the Sith are far more numerous. Sidious is one of three high Sith leaders, the other two being the merciful, ex-Jedi, political idealist known as Darth Clemence, - real name Yoss Vetter - and the cruel and vengeful Darth Grievous.
The Clone Army is already used by the Republic, having seen action in the “First Clone War”
No Qui-Gon, Obi-Wan is trained by Yoda.
Anakin is Anakin Lars. The name Skywalker is a nickname / call sign, fitting with his borderline-celebrity status implied by the PT Novels and with Obi-Wan’s description of him; “He was the best star pilot in the galaxy…” He is literally “The Skywalker”
Padme is a Noblewoman from Alderaan, as opposed to Naboo. After the end of the PT segment she raises Leia for a time with her close friend, King Bail Organa.
The Jedi aren’t good. The Jedi in the PT were quite evil in many ways, but it was somewhat ignored by Lucas and they were painted in a kinder light than what I think was needed. Instead of the Jedi being good, and the Sith evil, I’d like to depict them both as extremes, neither better, nor worse than the other. Both Orders are just as cruel and dangerous.
Anakin isn’t evil. In ANH we see a very evil Vader whom supposedly killed the good Anakin Skywalker. In ESB we realise they are one in the same. In ROTJ we see a sad and tragic figure whom became evil under unknown circumstances.
I would like to depict him as a good man, striving for justice. Fighting for a corrupt Republic and an unjust Jedi order, with a family that he wishes to protect and provide a perfect and peaceful life for. On top of that, he wants revenge and wants to right wrongs.
When the Jedi make the first move, he takes matters into his own hands, joins up with his mentor, Palpatine, and creates the Galactic Empire, believing it the best way to provide justice and peace to the galaxy. He then kills the Jedi, and the Sith - Palpatine betrayed his Sith allies. He brings peace and order in a time of war and instability. He is then punished for his actions by his closest friend and brotherly/fatherly figure, Obi-Wan.
For his troubles he rewarded with the loss of his family, the amputation of limbs, full body burns - likely causing the loss of his genitals, the loss of all round health, and loss of all happiness.
The Death Star isn’t in construction stages until long after the Jedi Purge begins.
Anakin doesn’t kill Padme directly, but rather harms her health enough to significantly shorten her life - ala Hal 9000 edit.
Obi-Wan exiles himself on Tatooine primarily for guilt. He has his hair in my version of the Padawan hairstyle as to show him thinking he made a mistake, feels guilt, and thinks himself to know less than he thought.