When we import our FaceFX FBX file into Unity and set the Animation Type to Humanoid to use Mecanim characters, only the jaw animation transfers over. Has anyone here gotten this pipeline to work? If we use Generic or Legacy for the Animation Type the facial animations work but we don't get to use any of the Mecanim features.
The jaw is the only facial bone in the mecanim skeleton. So you can't have mecanim animations with facial movements other than jaw movement.
The best you can do is use Mecanim for the body animations, and then use some other system for the facial animations. "Some other system" can be importing legacy FBX files like you suggest, or it could be our FaceFX controller script (see the unity forum link: http://forum.unity3d.com/threads/new-facefx-integration-with-unity.7807…)
Note that because Mecanim has a jaw bone, you will want to define your mecanim skeleton WITHOUT the jaw bone, so your other facial system is free to drive it. The head bone is mandatory in mecanim, but if you want to use FaceFX-generated head movements, you would need to use a different bone for mecanim and FaceFX (i.e. make sure your skeleton has something like: Neck->Head_MECANIM->Head_FaceFX->Jaw)