Make the clones of the eponymous wars the villains, as was indicated in the Thrawn Trilogy.
Give Windu and the other Jedi Council members their proper lightsaber colours:
Likewise, Aayla had a magenta lightsaber in her initial appearances in the EU. Gotta give that back.
Likewise likewise, the Dark Forces Trilogy mentioned that Qu Rahn’s golden lightsaber used to be Yoda’s. Gotta follow suit.
According to this story, Boba Fett was an alias used by the exiled Journeyman Protector Jaster Merell, not a clone of Jango Fett. I suppose it wouldn’t be too much trouble to rename the characters.
You do know all of those were explained at some point?