If I were in charge of a prequel story with Anakin Skywalker, I would not have him transform into Darth Vader during those episodes, at least, not fully. Instead, this would happen between the Prequels and the Original Trilogy.
Anakin in the PT is essentially Flash Gordon with a few notable changes. He comes from a farming planet in the colony worlds and is recruited to fight in the Republic Space Force by General Obi-wan Kenobi, who is secretly part of an order of Jedi Knights, reclusive warriors under the personal command of the Republic’s High Chancellor who are rumored to use a mystical energy source to achieve amazing feats. He is similar to Hans Zarkov except that instead of the magic of science, he uses literal magic that he implies is mere scientific trickery.
Obi-wan comes to believe that Anakin may be able to use this Force, and inducts him into the order of Knights, overriding the normal order of training where a Knight would be trained under a peaceful Jedi Master, one who had devoted their life to balance and tranquility. He confides with Anakin that this is not the first student he has had, and his prior attempt ended with failure. Nevertheless, Anakin agrees to the training. While training, Anakin and Obi-wan are tasked by the High Chancellor with protecting the planet of Alderaan. They are joined in this quest by a Republic translator and diplomatic envoy to Alderaan, who is to become the mother of Luke (A Dale Arden-style character). She is secretly a princess of Alderaan but she conceals her true nature from the Jedi in order that she could ascertain their true interest in the planet. For you see, even at this time Alderaan was wary of the increasing power of the High Chancellor, and they sought to protect their autonomy from the growing reach of the Republic Army and its secret service of Jedi Knights. Anakin and ‘Dale’ fall in love, but it is only Obi-wan who suspects her true identity. Having saved Alderaan, the trio go on to have many more adventures during the wars.
The wars rage on, with legions of genetically identical clones fighting the Republic forces. The Jedi are increasingly isolated since the old Jedi Masters now believe that the Jedi have become too warlike, and the Jedi recognize this as well. They distance themselves from the Republic, but even as they do so a mysterious dark warrior arrives and begins hunting down the Jedi. One by one, the Jedi start disappearing, always at the hands of this mysterious warrior. During the climactic battle for the Republic, the mysterious warrior appears in black armor to fight Obi-wan, claiming to be his prior student. He says that he is faithful to the High Chancellor, and that the Jedi have betrayed the Republic even in its time of dire need. Obi-wan say that the Jedi have given everything to the Republic, but this is not enough for the dark warrior. He strikes Obi-wan down, and it is believed that he is dead. Anakin hears of this and hunts down the dark warrior, finally fighting him above a pool of lava. They both fall into that pit and it is only at the end that we learn that Obi-wan survived. He goes to ‘Dale’ to tell her the news. he sees that she has a baby boy, and she gives this to him to be raised with Anakin’s family who are moving to the outer rim in search of a new home, escaping the war-torn desolation of their blasted homeworld. Obi-wan, seeing that ‘Dale’ is sick and not long for this world, goes to watch over the boy. The final scenes show that one of the warriors has survived the fall into lava, and returns to the High Chancellor to help rule over this new Empire that he has helped to create.
TL;DR: I don’t think that Anakin’s turn need be difficult or complicated. He was a simple man of action who fought in the wars for the Republic, in whatever form that government would take. Nobody bothered to ask him about his politics, and by the time anyone would have thought to ask it was already too late.