Well, I'd probably have made the films in general much darker than they were -- somewhere between Temple of Doom dark and Excalibur dark.
I wouldn't have limited myself to numbered trilogies, and would have made more than six films based in the PT & OT eras.
I would have kept Anakin Skywalker and Darth Vader seperate characters -- Anakin and Obi-Wan would have been about the same age and both trained by Yoda with Darth being a slave Ben rescued from a hellish Hutt-controlled planet and took on as his apprentice.
Luke would have remained Darth Vader's son. Darth either would have forced himself on Anakin's wife or had an extramarital affair with her; in either case, Luke would have been the illegitimate son of Darth Vader pawned off as Anakin Skywalker's.
More lightsaber colours beyond single shades of blue, red, green, and the occasional purple.
There would be no mention of Sith, Sith Lords, Dark Lords of the Sith, etc. Palpatine would be a non-aligned dark side sorcerer and Vader a Dark Jedi.
The clones in the eponymous Clone Wars would have worn pure-white Mandalorian armour and, obviously, would have been fighting against the Republic instead of for it.
Pre-bionic Darth Vader would have wielded a red lightsaber while bionic Darth Vader would have wielded a blue lightsaber.
I would have kept Clive Revill as the voice of Palpatine while casting a beautiful woman to play the actual character (I like creepily androgynous characters).
Han would have probably died, allowing Luke and Leia to get together.
Jabba's headquarters would have been based on a world of grasslands, not Tatooine.
No BS about Leia being Luke's sister. Another female character would have filled that role.
Only one Death Star, and only in the last film focusing on the OT characters, not the first.