Oct 18, 2017: This work around just became obsolete:
Character Animator CC (October 2017) has been released including:
"Copy a Lip Sync take of visemes (right-click on the take bar, then choose Copy Visemes for After Effects) as Time Remap keyframes for use in After Effects"
Character Animator has this nice feature to compute visemes from given audio, setting triggers for mouth shapes. In addition to animate the full character in CH, you could also just export the animated visemes with an alpha channel to After Effects.
But there is no option to transfer data or keyframes to After Effects, which would be nice for further or other use.
I just set up a preset as workaround. No magic, just a trick / brute force method. ;)
Instead of just animating mouth shapes, I expanded the graphic, so it will show marks at a specified position.
In After Effects, these positions get sampled and will trigger mouth shapes or other stuff. It is recommended to bake the expression though to improve performance, reuse the set up in the current scene for changed or additional audio and make the animations independant from CH at the end.
Character Animator means, you need to be subscriped to CC and have the latest beta of CH installed.
CS6 files are provided as well, if you want to use the custom mouth shape control slider, use the mouth shapes and have a look at the set up.
A demo folder is provided with a rendered image sequence, so the AE demo file will work without Character Animator.
Simple set up, but I tried to do a tutorial anyways. :D