How are you going to have side characters appear in your versions of the Prequels? Now, these are character who have a significant impact in all three installments, not just small cameos. For me, I'm going to do this:

Bail Organa

He's the Viceroy of Alderaan, who's trying to help rebuild the Republic after the First Clone War. To do that, he and Senator Padme of Naboo begin peace talks with the Separatists. During the Second Clone War, he joins the military and slowly builds the Rebellion as the Republic turns into the Empire.

C3-P0

He's a droid built by Anakin, like in the Prequels. However, Anakin hasn't completed him and 3P0's given to Padme, who uses him later on.

R2-D2

Just like his Prequel counterpart, he serves under Padme and works with C3-P0 to assist Padme. However, they will be more in the background than they were in the Prequels so the main characters aren't aware of them while allow the two droids to the observers as they were in the OT.

Owen and Beru Lars

Here, the two are a married couple who, with Anakin, leave Tatooine. They start off as traders, but with the Second Clone War, Owen and Beru return to start their farm on Tatooine (but not before failing to convince Anakin to join them).

Owen's related to Anakin, as in the Prequels, but it's also hinted that Owen and Obi-Wan are brothers. If I plan to go more into that, I'll say that Obi-Wan and Owen did come from Stewjon (as stated in Prequel EU) before Obi-Wan was sent to the Jedi and Owen went for Tatooine with his father.