How Anakin's wife fits into the story depends on the motivation of Anakin himself, if the prequels are about him. I think she should have some connection with Alderaan as you have said, but I think that it would be a mistake for her to feature as heavily in the plot as in the Lucas Prequels. I assume, based on ROTJ, that Anakin's wife was somewhat overlooked by him in the prequels. Perhaps the stories of the prequels could be more episodic than the OT, and she factors into only one of the adventures of Anakin.
I had an idea once about Episode 2, where Anakin and Obi-wan idealistically protect the planet of Alderaan against the more rational judgement of the Republic. They are outmatched because their troops retreat on the Republic's orders, and they are shot down over the planet. Obi-wan is separated from Anakin by hundreds of miles, and as the planet has little in the way of technology, Anakin is by himself in attempting to defend the planet against the forces of evil which beset it. He and the princess work together to rally the people of Alderaan and stop the invaders. Anakin is betrothed to a woman he met in Episode 1, but is seduced by the powers of the princess, and her promise of political power as a member of a royal family. The people of Alderaan have no weapons, but some have powers of suggestion and seduction (this is why Obi-wan tells Luke that he must learn the ways of the Force if he is to go to Alderaan). It is established by Obi-wan that seduction by the princess for the power of the throne is very much like seduction to the Dark Side for the easy power it provides. The audience believes that Anakin was not seduced by the princess, but the scene in question was cut vaguely, and it is only assumed that he spurned the princess for his betrothed. He returns to Obi-wan to fight the invaders by themselves, and they win the day. The incident is never mentioned again, and the audience does not know that Anakin turned to Vader. When Luke in ROTJ realizes that Leia is his sister and that he is also part of the royal family of Alderaan, the audience then knows precisely how Anakin was seduced and became Vader.