Apart from the decision that they were just going to do something new for its own sake (which happens often enough; OYL, for example), I suspect Cassandra got done in by being considered to out-there as a character.
That is, she's a quasi-mute (since she can speak now, but she's pretty taciturn still, when written well) former assassin trained since birth for the job. I'm guessing that when Didio and co. were evaluating what they want Batgirl to be, they hit on "normal American teenage girl", something Stephanie is a lot closer to.