Being a huge Star Wars geek myself, here's a challenge: We make sense of the destinations in the new Star Tours. I know that has been one mild complaint, that some just throw SW canon out the window, so, let's fan-fic this . I've only ridden once, so, I will only comment on what I've seen.
Kashyyyk: One of the easier one's, they wanted a speeder bike chase, but not Endor. Enter the Wookiees, who suffered the brunt of subjugation of the new Empire. This scene is detailing the last of the Wookiee uprisings before becoming enslaved. Think of them as Republic insurgents.
Coruscant: Now THIS one is a bit tougher. Despite ST2.0 taking palce between episodes III and IV, we clearly are thrust into a battle featuring Republic heavy cruisers and the Confederacy. Luckily, I do have EU stuff on my side. In Star Wars: Battlefront II, there is a mission in which a confederate loyalist activates a droid army, as another insurgency that is put down. Perhaps the Coruscant battle can be retconned as part of his efforts, or another branch of Confederate loyalists make an attack on the Imperial capital. As the ride takes place before the events of Episode IV, the presence of Republic ships can be explained that some have yet to be decommissioned in favor of more Imperail Class Star Destroyers. Ok, have at it!