This looks to me like one of the more promising & ambitious projects around, good luck and I'm eagerly expecting the results.
I'm actually working on an animation layering system at the moment. Where we can have a separate layer for the head and body to allow for interesting and unique expressions that the character may do while talking. Like putting his hands on his hips while his face is either angry or surprised. Or even just his head occasionally blinking while he stands around.
Huh, I exactly began working some time ago on a module that does the exact same thing (for use with my AGS Footballer, so that I would be able to compose characters using different heads, skin color, uniforms etc allowing me for endless amount of characters), I will probably go back to working on it again once I relieve myself of some other projects I'm doing, unless you will release your system, which would save me the trouble.
CaptainD having a child
Congratulations, CaptainD! Might I suggest naming the child CaptainE?