may I suggest another idea - make scales seem to pop out. May I suggest that you use a UV mapped normal texture and animate the normal strength (to make all the cales in a single texture pop out more or less, or, a bit more difficult, animate a mask or multiply texture that is blended with the normal map, you can move this around to make certain areas normal look darker/ lighter and even achieve a wave effect where the scales seem to bristle.
rigging thousands of individual scales would make me craz(y/ier)