I think I might have finally found a way to make characters more expressive during scenes than just being stuck with the handful of static expressions they have in the vanilla game. It involves some careful scripting, but I'm pretty sure it can be done, using the http://www.creationkit.com/ModifyFaceGen functions. The idea is that you create a script for each line of dialogue, which will manually controls the expression modifiers in use during that sentence, and attach it to the appropriate line when you create a scene. Rather tedious, but it seems like it would get the job done.
The one thing in the back of my mind that bugs me about it is how it might handle transitioning between expressions. I don't know whether it would be instantaneous, or if you'd have to create some kind of transition timer or something within each script to make each expression blend into the next one properly.
I haven't tried it myself yet, but I'm planning on doing it soon. If anyone has already tried it and can confirm whether or not it works correctly (if at all) please let me know.