The motivation for Stewie as Anakin would be to get some sweet Brian-Stewie screen time in episode I with Brian as Qui-Gon, that Stewie fits the evil bill, and that his relationship with the "fat-man" works with the whole Anakin and Obi-Wan dynamic, and that there could be a hilarious reference to Stewie Kills Lois as the Emperor tells Darth Vader that he killed Padmé, as well as when Obi-Wan (almost) kills Anakin as Peter did Stewie.
I'm 100% sure on every choice except one on which I need your input, and that is whether Chris and Stewie should switch roles or if this is the best fit. But if they changed their mind about that and decided to do them, this is how I would cast the characters: anyways, I was starting to imagine how I would cast the characters in episodes parodying the prequel trilogy, something Seth MacFarlane had said he "don't think" they will do. So I just finished re-watched the Family Guy Star Wars parodies of the original Star Wars trilogy, in reversed order, because I only intended to watch the last one while eating dinner, but then one thing led to another.