I believe that the current timeline should remain one universe, and patch it up as best as possible.
If an alternate universe were to be created, it would need to be from scratch. I'm thinking a new Infinities (for simplicity, call it "Ultimate") Episode IV adaptation, that is basically the same plot as Episode IV, but loosely adapted. Change the setting. Change some characters around (heck, switch some genders; it worked for Starbuck). Change all the little details, but have it in general be the same story: the Empire builds a weapon of mass destruction, and Rebels need to overcome incredible odds, use The Force, and destroy that weapon.
Like how the first 1-2 issues of Ultimate Spider-Man were a close adaptation of Amazing Fantasy 15. New setting, new relationships, new characters, but the same idea: Peter Parker is bitten by a funky spider, develops Spider powers, is ignorant of how to use that power, and it results in Uncle Ben's death.
From that first story, you can build forward and backward. You can make adaptations of all six films, but the ones that aren't Episode IV can be MUCH looser. You can change the entire geopolitical situation pre-Episode IV. You can do so much.
"Obi-Wan never told you what happened to your father."
"He told me enough! He told me you killed him!"
*Vader removes his mask, revealing that, inside, Vader is a beautiful, albeit very sickly, woman.*
"No. Obi-Wan killed your father. He was jealous of our love. I am your mother."
The trick is that any sort of Ultimate adaptation would need to be, at its core, Star Wars, but also significantly different from the rest. Otherwise, authors will just cherrypick their favourite EU stories and repeat them. You don't need the Thrawn Trilogy replicated in the Ultimate universe. Instead, you could have an author (NOT Zahn) use Thrawn in a similar way, but the hope is that the geopolitical setting would be so different that it wouldn't be the Thrawn Trilogy, but could be something else.
Prequels could be recreated in the same way. These would need to be significantly looser adaptations then even Episodes V and VI. You could invent almost any situation here, so long as it ends with an Empire and a Rebellion fighting it. You could take it back generations, have Episode II be the rise of the Empire, and Episode III be about a Jedi rebellion (with Obi-Wan and Anakin, and the aforementioned female-Vader, for example) fighting it.
So that's my take.
It was the year of fire… the year of destruction… the year we took back what was ours.
It was the year of rebirth… the year of great sadness… the year of pain… and the year of joy.
It was a new age. It was the end of history. It was the year everything changed.
The year is 2261.
The place: Babylon 5.