I think what would have added a little something to HC's performance in the prequels is if they modulated his voice a bit lower and lower as he turned more towards the Dark Side. Not to the point where he sounds exactly like JEJ during the final duel, but enough that the vocal transition from "Anakin" to "Vader" would feel a little more natural.

Over at FanEdit, there's a guy who just finished an edit of Batman Begins. One of the things he did was pitch Katie Holmes' voice down and in the before/after clip he posted, it makes a HUGE difference.