Thanks for the reply throttlekitty, it's a shame as it really means only experts will be able to make decent faces for Skyrim, I enjoyed the flexibility of older Beth games, I will keep playing with NPC faces though as I do enjoy getting a nice looking character in game. Maybe SKSE or SKGE will eventually allow us the control that's missing in the CK.
In a similar vein to what rdm is talking about, I'm considering making a blender file to this end. It would have a head and a set of morphs with as easy to use controls for it as possible. Players would use this in conjunction with the nif exporter to create a game-ready head for a customized race. -Essentially an expanded version of what the game currently offers.
The downside to this is all the things that need to be installed to get blender + nif export running, and following a tutorial to do the face morphing and export process. Perhaps a bit much for the average person?