Hmm... Well if we're talking canon characters, it would have to be Amelia. I've used her as my main the longest, and she's the only one of the main cast to actually flip alignments should the cards fall in that way. I assume that would kinda be the biggest transformation since it's so distinctly out of character... kinda.

With fancharacters, I'd probably say that Sakura going from shy farmer to sex-positive love guru is a pretty big shift.