There was another weird Star Wars Story that retold the first trilogy (4,5,6) main story but changed it in strange ways. One was that Darth Vader lived. I didn't collect comics back then so I remember reading the last episode with Vader alive all in White instead of black, and I wanted to read more to see if they could tell an interesting story with Vader being good.
If I was to do a What If Star Wars Story, I think the story arc I would follow is Samuel L. Jackson's Jedi killing the Emperor in that Battle, and Anakin witnessing the slaughter of an old man that he believed was his friend. It fueled a hatred for the Jedi order that made them look evil. The death of the Emperor leads Anakin to turn the senate against the Jedi after he renounces their ways, and the senate orders Order 66 as an official vote. After Padma gives a stirring speech against the Jedi after she talks to Anakin. This is a far more compelling story.
You have the problem of the Emperor not being the the original series, but that What If story could be that Darth Vader takes that role after he is left for dead by his master. Or you have Samuel L. Jackson's character having killed a clone, and the Emperor saves Anakin revealing he did this to reveal the truth that the Jedi council is not so righteous or "good" that the dark side is not an evil...making Darth Vader a true believer.