Animating faces from motion capture

After Effects has a fairly sophisticated face-tracking system, but nothing as automatic as the mobile phone apps.

Character animator is a useful tool for creating flat 2D animation. You can easily make a character walk left or right in profile or face the camera, but getting characters to walk from upstage left to downstage right is a real problem. Making characters spin around is also problematic, but it is a lot faster than creating all the in-between frames by hand. You basically create a pose to pose Illustrator or Photoshop document with all of the poses arranged properly in overlapping layers, then Character Animator will create the tweens between the poses. Character Animator also has "bend the mesh" behaviors that make it a lot easier to animate things like walk cycles. It is similar to rigging a 3D model, but again, it is only 2D.  Character Animator is a separate app, but you can bring Character Animator files into AE for final compositing.

If I was tasked with creating a lot of animated facial features I would probably look for another app to automate things. I don't use those filters and I don't know if any of the mobile apps let you use recorded video, but that's probably the first place I would look. If you are going to use After Effects and you want things like floppy ears you are going to have to create the floppy ears in another comp and somehow tie the floppiness to some kind of control to get the kind of interaction that a mobile device can achieve with facial recognition + the accelerometers in a mobile device. If it was my project I would budget about a week for research and testing before I committed to a specific workflow. AE's face tracking would be the core.