But if the whole point of the prequels was to follow Anakin's transformation into Vader
Ah, but that was a mistake. Star Wars is, at its core, first and foremost a space adventure saga, not a Shakespearean one-family drama. The main point of the PT should have been the Jedi's struggles against evil, orc-like clones and the Dark Side sorcerer leading them, and the increasing violence of Anakin (a real "If you gaze long into an abyss, the abyss also gazes into you" situation), along with the surprise reveal of Palpatine's own evil, should have been the secondary story.
And no, there was no need for Luke and Leia's mother to have been a primary character. Obi-Wan's flame could and should have been the PT's main heroine.
Bottom line: I respect Lucas' thematic intentions for the PT, but, in terms of narrative and story structure, not to mention basic character dynamics, he got almost everything wrong.