What do you mean by cut scenes? When and where? I don't mind the additional work, as this is the stuff I've been waiting for, but knowing where and what we're thinking would be helpful.
My general thinking with the questions isn't so much a branching bimbo route, but one that encourages her to act out, at least a little bit. That's why more weight is given to the S-Links that encouraged a more positive approach to the changes. For now, I'm thinking that continuing to work the Twilight/Pinkie angle is most helpful, although that's certainly up for discussion this early on in the Links, and even going forward as well.
I like the idea of having to change Velvet too, just because it forces the Player to indulge in using their power a bit more. Kind of like the one where Twilight freaks out earlier. Something similar could be done with Cheerilee or Pinkie Pie as well: depending on how involved we want to have those characters.