My prequels ditch R2 and 3PO, as well as a number of other pointless OT pandering characters like Chewie. Yoda only appears briefly in Episode III, and in much the same capacity as he did in the OT. Not to mention the same location.
I've eliminated basically every single character, setting, and plotline from the existing PT. You will never *ever* hear about Mace, Jango, Maul, Grievous or any other obvious toy-making cash-in characters or comic relief for babies.
Same goes for one-off villains who are given no background of interactions with our heroes or any personality to speak of. There's only one major villain in the series besides Palpatine and Vader, and she's a former Jedi herself (who happens to wield the same red lightsaber that Vader uses in the original trilogy).
And most importantly, I've done my best to eliminate anything having to do with "Senate negotiations" or "taxation of trade routes". Those kinds of boring terms make my eyes glaze over.
Also, Anakin's love interest does not have a profession as boring as being a Senator. She's a rock-and-rolling star pilot badass like her son will be and her husband always was.
Don't get me wrong, I understand that there must be some kind of political background to galvanize the events in a remade PT and thus set up the OT, but I try to do it in a more interesting way.
In my version, the Clone Wars are a racially-motivated conflict. Alien species from many star systems break off from the Republic because they feel that Humans unfairly dominate the galaxy. So these aliens fight against the Republic, bolstering their numbers by cloning the best warriors of so many different races.
In doing so, I believe I have created an adequate justification for the general marginalization of aliens in the OT.
It kind of amplifies the whole "Empire = Space Nazis" angle, does it not?
Finally, I couldn't write my way out of having two protagonists. But this time, it's not Anakin and Obi-Wan. Instead we have Anakin and his apprentice Ben. This being the man who Obi-Wan Kenobi names himself after while in exile on Tatooine.
It's kind of a long story!